Well, the people to talk to for all the details would really be Komuna and Zayford. However, I can give you the info 2nd hand, in brief.
First off, wow, that must be some amount of scripting to run into the savegame bug without any external scripts or addons! The ECP only has that bug when running on top of missions with heavy scripting, so yours..... must have quite a bit.
Basically, the way that Komuna managed to "fix" that bug is by transferring all of the global ECP variables into just a few global arrays. It seems that an array, no matter how large, only counts as "one variable", in terms of how many variables the mission has running. So instead of having 100 global variables, you plop them all into a single array and you've cut it down to 1 global variable.
Of course, this makes things rather inconvienient in terms of scripting, because you have to remember, "ok, (GlobalArray select 24) is the difficulty setting....", but oh well.
I don't remember what Komuna did (or didn't do) in terms of local variables, or if they had the same impact as globals. I could go dig up some threads from the ECP board if you want, or, better yet, Zay or Komuna can pop in here and give you the whole story.