I wouldn't want to work with 90 instances inside of one VEPro Server. VEPro was never intended to be operated this way. Perhaps you are better off using 16 MIDI channels per VEPro instance, then spending some time with VEP automation, mapping the relevant parameters?
In any case, VEPro should not crash when opening projects, even when instance counts are insane. I just tried 60 empty instances here, saves and loads just fine. If you have a crash report for me to look at, please send it to support@vsl.co.at.
It is unfortunate that Logic still has this issue with Aux tracks and core-spreading. Hopefully they can address this issue, because it apparently causes some pretty wild workarounds...