A larger naval presense in Vladivostok and a smaller one in Port Arthur could have made a lot of difference too - cruiser squadrons raided Japanese transports despite Japan locking in the bulk of the Russian navy.
That would have made for a very nerve wracking war on the Japanese side. Russia even had a few submarines in the Far East too.
While torpedoing freighters is asking a little too much for the period, I've always wondered what a submarine mine laying effort could have accomplished. Japan lost two battleships, something they managed to keep hidden while the war was still being fought, to mines around Port Arthur.
Of course - Port Arthur was lost because Dalny was lost (huge numerical disparity for the Japanese)...
Agreed. Holding Dalny allowed Japan to ship in the 11-inch mortars which performed most of the heavy lifting during the siege. Much more importantly, Holding Dalny allowed Japan to land and supply Nogi's army besieging Port Arthur
and Oyama's army group operating in Manchuria against the Russians. Neither force could have been supplied solely through Chemulpo (Inchon). Dalny was a necessity and delaying or preventing the capture of Dalny would have had huge consequences.
... and then the approaches to the heights from where the Japanese could siege Port Arthur was lost again (60K vs. 16K).
Even after Port Arthur was lost to Russia as a fleet anchorage, it still could have tied down Nogi's 3rd Army. With her main supply port of Dalny so close to Port Arthur, Japan could not leave that Russian garrison in her rear. There were also psychological issues in play. Nogi had taken Port Arthur with little effort in the 1st Sino-Japanese War and was now fixated on taking the port in this war. Like a degenerate gambler throwing good money after bad, the increasingly suicidal Nogi kept squandering his troops in frontal assaults in an eerie prequel to WW1's Western Front.
Nogi was able to begin bombarding the harbor during the first week of December, finally took the last large prewar fort on the 31st, Stoessel surrendered the next day. After taking control of the port, the Japanese were shocked at the number of troops, sailors, and supplies still available to the Russians.
After losing perhaps as many as 100k men killed and wounded, Nogi was able to shift his roughly 120K man army north to join Oyama just in time for Mukden in mid-February. When you remember just how much a close run thing Mukden was, you can't help but imagine what might have occurred during that battle if Port Arthur held out for less than one month more.
There were lots of bad land decisions as well as bad naval decisions.
Again, agreed. As with the loss of Makarov, single deaths like that of Kondratenko had huge consequences.