Bad skill modifiers is an intrinsic EA flaw, where damage accumulates over time, due to the really hokey way EAxis accumulates skill modifiers, which is, frankly, awful. We presently do not have a preventative solution that will reduce the incidence of bad modifiers, only a fixer for it afterwards.
Haven't played since ambitions and just got the missing ui/sim/naked sim issue when playing in bridgeport. Though I saved often and under different names, about half of them were borked. Found out the hard way I have to double check my save files as well as use fixall.
On that note, decided to play around with fixing an old working save file and your mod found 300+ bad skill modifiers along with 3 bad butts (lul).
First time saving after fix, the game borked and did an immediate CTD. Tried again and it seems ok though I expect it will CTD again.
Anyways, the game must be allergic to working code. It never CTDed when it saved 5 thoroughly f*ed up files....