From what I've read, the more you save the bigger the chance of getting a corrupt save witch in trun 'can' give you CTD's.
So only save when:
A) There's no land close to you (within 20Nm should do).
B) There's no sonar, radar, Hydro contact.
C) You're on the surface going ahead standard.
D) If you used TC pause the game and wait 10sec then set normal time.
E) You've checked every torpedo has been loaded.
F) You're not still running silent.
G) You're in the control room (you start there anyway).
I found when forgetting one of the above chances are there will be a corrupt save somewhere in that campaign.
Obviously MOD soups can cause CTD's and are the most common reason for them but when taken every precaution very rare.
A hiccup from JSGME could also be the culprit and you'll never know if that has been your problem.
Got a couple of question's for you:
Did you try out different MOD's before you ended up with the soup you have now?
And, did you have JSGME check your files (via a snapshot) after changing those soups?
I understand if you'd rather not do this but I'd recommend a clean sweep, delete the JSGME/MODS folder and replace your Data folder if possible.
Than create a new MOD's folder and
create a new snapshot of the new Data folder before installing/activating anything, then reinstall your mod soup one at a time.
Do not cut'n past the MODS folder out and in.... create a new one and put freshy unZiped MOD's in there, no copying them from the old MODS folder either!!!
As I see it JSGME is a pretty stable tool but combine it with a very unstable program like Silent Hunter you're gonna get hiccups and being very meticulous when installing/activating or deactivating/uninstalling mods gives you a better chance of succeeding in getting a stable platform.
Call me paranoid
but this keeps me from having CTD's and corrupt saves.