I have been through this several times and you really need major changes in order for the Kalmar Union to survive.
There were major differences between the interests of Sweden and Denmark.
1. Denmark was moving towards continental serfdom - not fully so, but their peasant class was almost landless and had little power. The Swedish peasants were mostly free-holding (52% of the arable soil in Sweden in 1500), had rights, were required by law to keep and train with arms, The Danish nobility, and especially their German mercenaries were not used to deal with free peasantry. The Danes often placed their German mercenaries as tax collectors (akin to an English Sheriff) as a reward for their service, with the non-written agreement that anything they could press out of the peasants that did not belong to the crown, they could keep. Many of them were quite surprised when the Swedish peasantry showed up and burned their forts.
2. The Kalmar Union lasted in name only after Margareta's death. Sweden was at a constant civil war, between nobility that supported the Danes, the peasants and nobility that supported Swedish strong-men, usually of the Sture house, but also Karl Knutsson Bonde. Every Danish King had to force the Swedes by arms to crown him King. Sweden was a drain on Denmark's resources, not an addition to it.
3. Swedish interests lie in the east - against the Teutonic Order and Novgorod, trying to get more of Finland under her power. Denmark's interests lie in the south, with Pommerania, Schleswig and fighting the Hansaetic Legue. The Swedes have nothing to gain from aiding the Danes and the Danes have nothing to gain from aiding the Swedes.
4. The Hansaetic Legue would support any revolt inside the Kalmar Union. A strong centralzsed government controlling the Sound (and its toll) and trying to control Hansaetic trade cities such as Bergen and Visby was bad for the Hansa. Gustav Wasa got the ships and cannons he needed to take Stockholm from the Hansa. As long as the Hansaetic Legue benefits from the Kalmar Union being weak, they will add their considerable resources to any revolt. In the long run, this role will be taken over by England and the Netherlands, who need the tar, hemp and wood that is produced in Sweden and Finland and carry substantial trade on Polish and Livonian grain.
Let me give you a short run-down of the Kalmar Union:
1397: Erik crowned King of Sweden. By now King of Norway, Denmark and Sweden, with Margareta as regent. Margareta promises to respect Swedish laws and keep Swedish nobility as tax collectors. In an effort to strengthen royal power, she started to reduce the land ownership of the nobility. German and Danish tax collectors and a habit of appointing bishops herself had already alienated the peasants and much of the church. Small local risings happen now and then. They are mostly defused by negotiations, in which the nobility have to promise to respect the peasants' rights.
1434: First major revolt. The Engelbrekt rising. Citing forced service in wars abroad, Erik appointing bishops instead of the pope, high taxes, violation of the agreement in Kalmar regarding who will be named tax collectors, high tolls and no respect for the peasants' rights, the Swedish nobility and peasants rise almost all over Sweden, defeat the King's forces and declare him deposed (according to the old laws in which Swedes own the right to take Kings, but also to depose them). The revolters soon controlled all of Sweden, a lot of forts and castles being turned over to them. The King is forced to appoint the leader of the rising, Engelbrekt Engelbrektsson as Chief Chancellor of Sweden. Negotiations ensue, but Engelbrekt Engelbrektsson is murdered with an axe the next year in an internal dispute with another Swedish nobleman. The revolt petered out and Erik was re-affirmed as King in the negotiations. The King is forced to appoint Drots and Marsk (chancellor and military commander) from the Swedish nobility.
1436: Since lots of the issues were unresolved, revolts keep happening and the parties meet again in 1436 to negotiate. Erik is forced to sign a new union agreement that looks almost exactly the same as the one in 1397, but with an addition that the countries are separate entities and should rule themselves as much as possible. However, continued negotiations in Söderköping and an extensive agreement on how the Union should be ruled was ignored by Erik and the Swedish nobility started to appoint tax collectors themselves, which Erik did not approve of.
1440: Erik got into conflict with the Danish nobility, who deposed him as he tried to have his cousin Bogislav of Pommerania named heir. Christoffer of Bavaria was elected King instead, and confirmed after negotiations and crowned in Sweden 1441 where he promised to respect the old rights. Erik retreated to Gotland and terrorized the Baltic Sea with a fleet of pirate ships for the next eight years.
1448: Christoffer dies, and Karl Knutsson Bonde is elected King in Sweden, while Kristian of Oldenburg is elected King in Denmark. Kristian has to go to Norway to fight to be named King there too. 1449 Karl Knutsson Bonde is named King of Norway. Karl invades Gotland and takes Visby, but Erik trades the castle of Visborg to Kristian and the Danes.
1450 in negotiations both Kings agree that when they are both dead, a new Union King for all three countries will be elected. Kristian is crowned King of Norway.
1457, Karl is forced into exile after a revolt by Danish-minded noblemen. Kristian is crowned King of Sweden.
1458, Kristian is named Count of Schleswig and Duke of Holstein at the cost of 123 000 Rhenian gyllen. The price means new taxes and with them new revolts in Sweden 1463-1364. Karl returns and is successful enough in the new civil war to be elected King 1464-1465 and 1467-1470. Second half of the 1460s is one long, bloody civil war with the spice of constant peasant risings.
1470, Karl Knutsson Bonde dies and Sten Sture is elected Chief Chancellor. Kristian again tries to claim the Swedish crown. 1471, Kristian lands in Stockholm with a large army of mercenaries, with cannon and arqebuises and is decisively defeated by the Swedish peasantry led by Sten Sture at Brunkeberg. Probably the finest moment of the Swedish peasant armies.
1476, negotiations started and Kristian admits that the Swedes have the right to revolt under some circumstances (!). However, in the end, the negotiations are unsuccessful, Kristian is not crowned King of Sweden.
1481: Kristian dies and is replaced by Hans, who can rather quickly confirm himself as King of Norway and Denmark. Negotiations start in Sweden.
1483: The negotiations finish, Hans will have to admit the rights of the church, the peasantry, the nobility, all things Kristian and his predecessors agreed to and many other things, and he shall be crowned King of Sweden. Hans does not turn up, probably because he finds the deal far too outrageous to agree to.
1497: Renewed fighting between Sten Sture and Hans. Sten Sture and his peasant army is defeated at Rotebro and Hans is crowned King of Sweden after negotiations. The Danes place Danish and German tax collectors in Swedish castles again to reward the mercenary army that won at Rotebro, causing widespread dissent and discontent.
1501: The peasants and nobility rise again. It is from this campaign that Paul Dolstein drew his pcitures of German Landsknechts fighting Swedish peasant soldiers. Sten Sture dies 1503 and negotiations were started again.
1505: Hans lands in Kalmar with representation from the Holy Roman Emperor, executes some of the local burghers, puts together a court that judges all the Swedish nobility as guilty of treason and crime against the majesty, with the support of the Imperial representatives. New negotiations takes place as the Swedes refused to abide by the court's decision.
1509: The Swedes admit that Hans has a right to the Swedish throne and that Sweden shall pay a tribute.
1510: The Swedes refuse to pay the tribute, and war starts again. 1512, Svante Nilsson, the leader of the newest rising, dies and new negotiations take place. A new meeting is to be held 1513.
1513: Hans dies. in Sweden Sten Sture (the younger) is elected Chief Chancellor. The Swedes refuse to either pay tribute to or elect Kristian II of Denmark as King of Sweden and fighting breaks out again. Sten Sture (the younger) is wounded in the decisive Danish victory in the battle on the ice of Åsunden 1520 and dies soon after.
1520: Kristian II is after negotiations elected King of Sweden. Promising amnesty as part of the negotiations, he holds a great feast in Stockholm and then executes a lot of the nobility he has promised amnesty in the Bloodbath of Stockholm. He then leaves for Denmark early 1521. Southern Sweden rises in spring, central Sweden follows in summer and Gustav Wasa is chosen to head the rebellion. After two years of fighting Gustav Wasa is victorius and is elected King 1523.
Now, this is a very short description of the massive mess that was the Kalmar Union. You tell me if you can get this pile of crap to work as a state in any fathomable way.
The Union lasted 126 years. The Danish King was in control of Sweden for a grand total of 56 years. Of them, 37 years was in the beginning under Margareta and Erik. The Danes needed to negotiate and fight all the time to keep Sweden and in some cases Norway too, under control. You need to address this if you are going to make a time-line where the Kalmar Union survives. How do the Danes keep Sweden under control? It matters quite a bit for how the Union develops.
My take? You need to get the Oldenburgs and their interest in northern Germany out from Denmark. You need to stop the enserfdom of the Danish peasants, so they keep being a power factor - the Danish and Swedish peasants usually saw eye-to-eye and made local truces in all wars from 1300 to 1800. the Union Kings can then ally with the peasants against the nobility and start building a centralized state (as in OTL in Sweden).
You need to avoid revolts and wars as they fed the need to pay the mercenary army, which made it necessary to place its commanders as tax collectors, which fed more revolts etc. It is too early for a professional national army, and any kind of militia will be more loyal to its region and old rights than towards the King. It is also only effective in its native terrain. This problem is probably the hardest one to solve.
You also need to make the Danes and Swedes see eye-to-eye on a Baltic Empire. Fighting the Teutonic Order and Novgorod should be in the interest of Denmark too, and you need the Swedes hating the Hansaetic Legue like the Danes did. Common enemies do a lot for unity.
You need to weaken the Hansaetic Legue and later the Dutch and English, as both will be interested in a break-up of the Union to balance the strangehold the Union King will have on Baltic trade (both Livonian, Polish and Russian grain and tar, hemp and lumber from Sweden and Finland).
The scenario was, at many times like this:
Danish, German or Frisian mercenaries manned the local fort, under the command of a lower nobleman or a mercenary captain from one of those countries.
The leader needs to pay his men, he also wants to get some money for himself and has his position as a rewards. Some pressure, like with the serfs at home, will surely make the stupid peasants pay up.
Winter comes, the peasants have collected their harvest, chaffend and milled it and the mercenaries are about collecting taxes. The peasants learn just how much the mercenaries want and get upset. They complain, someone gets beaten and then things go to hell in a handbasked. The peasants, done with the harvest and with the ground nicely frozen, take down their arms from the wall (this included, by law, crossbow or bow, sword or axe, plate or chainmail, helmet, spear and supplies for three weeks). Hunting was free in Sweden, meaning every peasant knew how to use a bow or crossbow, and in many cases also arqebuises. A leader was elected and the peasant host started out on skis and sleds to deal with the mercenaries.
The mercenaries in their fort is in shock. Peasants are not supposed to be armed, especially not this well and they are absolutely not supposed to be experienced and trained in the usage of those arms. And they should not be this organised. If the mercenaries are organised and mounted, an ambush is set in the woods, felling trees over them before cutting them down. Otherwise, the fort is put under siege and burned down (it was almost always wooden). Nearby villages hear of the revolt and happily join.
Now, the peasants don't need to go home before spring, and move easily on skis and sleds over the frozen and snowy ground. The mercenaries are slowed down by the same snow, the risk of ambush and cannot count on support, as roads are snowed in and all ports are frozen. By the time the Danish King can send reinforcements, the peasants have had six months or so to take all forts etc they want to take.
This happened again, again and again during this era. The Swedish peasants were experienced veterans of seasonal warfare, well-equipped and above all knew their own power and would organize armies whenever they thought it suitable.
Find some way of keeping Scandinavia as one political entity. POD after the establishment of the Kalmar Union.
