On first look at your mod list, you should install these mods in the following order (though I don't think it's causing the problems you describe, the new order could prevent problems further down the line):
IRAI
FX Update
New UIs with TDC.
The warship (friendly or enemy) following you about is a stock bug I think, one we all get from time to time. The only thing you can do about it is wait until he gets bored and goes away, sometimes attacking another ship or similar actions reset the bugged AI.
The CO2 on surface/deck watch not in conning tower problem is another stock bug, but one with an easier fix. Just save/reload and your sub will act as surfaced again and vent all CO2 etc. Used to happen in SH4 occasionally as well.
