As a Hispanophile I really like this timeline, but there were a few things that seemed inaccurate and/or ASB.
First of all, the numbers you use for armies are way too high. Those are 20th century numbers, not 16th/17th century ones. 500K+ men in battle? No way. The only those numbers would make sense if you were writing this TL in the form of a contemporary account (which tend to greatly exaggerate army numbers).
In chapter 2, the peace treaty between Spain and France states:
...
yet in this map Spain is shown holding the whole of Occitania, not just those three towns/regions. If Spain were given only those three towns the border would look
something like this.
Also I doubt the French give Picardy to Spain, which would leave the gates of Paris wide open. France is strong enough to hold its own against Spain. If they were allies, it would be an equal relationship, not France becoming a virtual Spanish vassal like the TL suggests.
However, these were only minor mistakes; the real Alien Space Bats come in Chapter 5.
While Spain defeating Morocco is possible, conquering the country is a whole another story. At best they'd be able to control the coastline + the area around Marrakesh. They wouldn't be able to extend in Mali like
this map shows.
Then Chapter 6 is almost completely ASB. Crusades were a thing of the past; I understand the symbolic naming of the "Tenth Crusade", but it would be nothing like the medieval crusades. 50,000 Catholics wouldn't join the Spanish just because it was a Crusade. If those men were mercenaries, it would make sense, but otherwise no.
The march from Algeria to Egypt and beyond would not be possible. 17th century technology lacked the logistics to march 100,000 troops across the North African plain and Atlas Mountains. A march across Algeria alone would be decimated by disease, heat exhaustion, and attacks from the hostile locals.
Taking North Africa would be possible if the Spanish defeat the Ottomans at sea a la Lepanto. They then could ferry their army from coastal city to coastal city, establishing footholds, effectively destroying Ottoman authority in the area.
While taking North African cities would be relatively easy, Egypt would a tough nut to crack, along with the Levant. At best, the Spanish would be only be able to control Alexandria, the Delta, and
maybe Cairo and the surrounding area. Even if they defeat the Ottomans, they would not be able to send an army of 100,000 men down the Nile; disease alone would decimate them.
This map is completely ASB. First off, the base map you used looks like it's from c. 600 B.C., not 1600 A.D. Secondly, a march across the Hejaz and Syrian desert is mostly impossible for Western Europeans at this point. Also, Babylon was a ruin by then, taking it would mean nothing (besides, the Ottomans would have destroyed an army attempting to advance into Mesopotamia at this point).
Landing an army in the Levant is not possible unless the Spanish have some kind of Eastern Mediterranean base (most likely Cyprus, but it would be a helluva fight trying to capture that island). From there, they could station their navy+army, and launch a landing on the Levant. Taking the coast and Jerusalem is probably the extent of Spanish success in the Holy Land.
Taking the Holy Land is one thing, keeping it is another. No doubt once the Spanish pull their troops out the Ottomans would overrun it. It would be a nightmare attempting to keep it under their control, Islamic rebellions alone would probably undermine Spanish control.
In the map above, Spanish also appears to hold Mecca and Medina. Again, this would not be possible through a land march. The only way it could happen is if the Portuguese launch a naval invasion from Aden that captures Jeddah and subsequently those two cities. I imagine the taking of the Islamic holy cities would be a major event for the Catholics, and you don't seem to mention it at all.
About the German Holy Wars, the Protestants would never invite the Ottomans to invade. Muslims are infidels in their eyes, and they would take Catholic rulers over Ottoman ones any day. In fact, whenever the Ottomans attacked Austria the German States forgot their religious differences and joined together to fight them off - there were many Protestant troops fighting on the Austrian side during the Battle of Vienna in 1683.
The battle of Vienna in this TL wouldn't actually take place in the city. There were walls protecting it. Besides, the destruction of Vienna like you said would be a complete disaster and counterproductive to the Habsburg agenda.
In conclusion, these are the things I saw as improbable, and my suggestions to fix them:
1.) France should not be a Spanish puppet. They are a power on their on their own. Any alliance between them would be an equal one.
2.) Bring down the army numbers a bit (unless you are writing this as a contemporary account of events).
3.) The Spanish conquest of North Africa wouldn't be a march across it. Have the Spanish defeat the Ottomans at sea, then the Spanish would be able to besiege and take all major Ottoman strongholds in North Africa.
4.) For the taking of the Holy Land, have the Spanish invade Cyprus first, thus giving them an Eastern Mediterranean base. From there they could take the coastal strongholds and Jerusalem at best.
5.) For Egypt: taking Alexandria and the Delta is the best the Spanish could do. Possibly Cairo, but that would require a major engagement with the Ottomans, in which the Spanish would have a major disadvantage and would probably lose.
6.) Any land-grabs from the Ottomans in Arabia would be done by the Portuguese through their bases in Aden and Hormuz.
7.) The Ottomans should not be allied with the Protestants in the German Holy Wars. If they are involved at all, then they would be a third party. Any engagement around Vienna would not take place in the actual city and the Habsburgs would go through great lengths to make sure the city is not destroyed.
Just to clarify, I have enjoyed the TL (except for the points I mentioned), and I want to see it continued, but in a realistic way.
P.S. If you need help with maps, I can create pretty decent maps.