Tried updating to just Vilja 3, without the custom version, and got the same result, game crashes as soon as I try to load any save. Tried without the FCOM fix file as well, same result. Switched back to 2.0 bsa and 2.3 esp everything fine again. Will try again once I get out of the last HOD dungeon and see if that makes a diff, Vilja is not in the HOD dungeon with me. Have not made my own custom version but have thought about making a Vilja as TangMo version just for the humor aspect.........Think I will try a Kaleen version once I get the update sorted out instead though.
I wonder if maybe some other mod has added a scripted token to her and that's the reason why it doesn't work for you? We have been testing so thoroughly, I really cannot understand why you get CTDs when updating, scripted tokens is the only thing I can think of.
Now, if you are really, really, having problems with this, I think one of the new features in Vilja 3 will be very helpful for you. If you should be forced to uninstall and reinstall Vilja, you can go to Heneri in Cheydinhal and cast Vilja's Start Combat-spell on her. Vilja won't attack her, instead you will get a messagebox that will allow you to set Vilja back to approximately where you were in the storyline. This includes updating topics, giving you a summon-spell for a certain animal companion, and setting her story about herself and her committment to you properly (well, at least approximately).
Still, see if another mod might be the reason for your difficulties. If you have anything that could have given her a scripted token, I imagine this could be the reason. (I suspect CDCooley has more (and maybe better) suggestions on this, but he's in the states and probably at work at the moment).