Welcome back Spectre,
1): With the new TWoS version it should be easier to setup SH5 with Uplay or Steam, but that's all I can say about. I play without them and my game loads almost instantly (i7 4ghz, 16 GB VRAM).
4): You should max-out pretty everything in your game options, especially if you play with Real Navigation. I play without RN to be more flexible to make changes in the OFEV, I have maxed-out all difficulty except the in-game map automatically showing spotted enemies, for me it's a game, I don't want it too real, it can get quite difficult enough even with that...
5): Don't know exactly what you mean here but if you play RN then you must rely on asking the Navigation man to plot your position on the map , plus you must rely on 'Supermarks' and saving them, also because every other things you mark on the map will disappear once you quit the game.
Cannot say too much about your other points, but feel free to find and read the guide I have made about starting TWoS anywhere in the campaign, so you can plan to encounter and you won't miss historical events if scripted by WoS.
Have fun,