I have virtually the same Mod list as you. I eliminated the crashes by first adding the SH4.exe to the Large Address Aware program, adding the 4Gb patch for good measure, and following an old protocol for saving that includes always saving from the Control Room view (F2), and waiting a bit (30 seconds to a minute) for the game to fully save to disk (it's not instantaneous). I actually watch my disk activity light to make sure the major activity has stopped before hitting the Resume button. The only times I will lose a Save game (unable to reload) is one taken near the end of a patrol that had a lot of activity (many sinkings), and I think that too is because I did not let the Save activity complete before exiting or moving on.
This all may be anecdotal, and the software engineers out there may say it is all superstition, but it works for me. Like many suggested, I (almost) never overwrite a previous save, using the game's date as the key save name feature. Good luck!
