Im using a similar mod list, I have most of the same weapon errors as you do, and I havent had crashing/save problems since I allocated 4GB, however I'm about the same number of cycles into the game as you and things are taking a hella massive performance hit. I have a strong feeling it has to do with the large number of fleets being spawned by Nexelerin and all the invasions and what not going on, but more specifically, the Debris Fields.
I've noticed that because I keep defending stations, which will take place in multiple battles with the insane number of ships that were being sent, generating massive debris fields that yield thousands of supply. I feel like they may be linked since the game seems to keep track of everything that died to make each debris field, to keep generating rolls off it, since it seems actually salvaging from them, makes the performance issues worse.
Also playing into this notion of mine is the fact that these mods are adding ship hulls, weapons, LPCs and hullmods to the data that needs to be stored for debris fields.
Performance seems to pick up some when I let time ride out without generating much more debris myself, which I assume is from the fields dispersing.
This is all speculation and could be coincidental, or only partly related, but my mod list is on the shorter side than many I've seen here and the hits I'm taking in performance are crazy, but they clear up when I reload the same save that was chugging prior.