Nice sub career you have there Urge, and THAT is the way to ask for help when one wants an answer. Plenty of information for others to work on.
Doing what sober adviced above is a good start. On top of that I'd also disable Temporal AA and Adaptive AA completely(leave "normal" AA at 4x) and see if improves things. What comes to your time compression problems and other times when SH4 seems to be "lagging" for some reason, it usually helps to go to map view and pause the game, then Alt+tab out of the game, wait a few seconds, Alt+Tab back and continue playing.
Welcome to Subsim
