It should be given in triangles because game engines triangulate meshes, that's simply how they work. A game engine has a budget for assets, there's a good reason to keep it within limit. Since you're making this for yourself, you should be ok and not lag anything to death, but you'll get "vertex shading error" for sure.
The 7k mesh you have is probably 14 000 triangles, that is HUGE for a game like JA. Just to put things in perspective, 14-20k is not uncommon for current games.
We didn't make the animations compatible and they worked just fine, you should probably keep a root pose a frame 0 (default pose at the start, that is needed if you plan on mixing multiple XSI files into 1 .GLA).
Forget any kind of heavy single player modding...the minute you need code to be added you won't be able to do anything, the source code was never released and will never be. Jedi Academy was built with vehicles in mind so i would stick with it, there's still no source code for JA either.
We did not make separate files, only one file was exported, which contained all the animations, the start and end of each was simply assigned in the .frames file.
The only animation i was able to watch came from the wampa and tauntaun i believe, i think i used something called "crosswalk" which was used to transfer content between XSI and Max, not sure if the old versions are still available online.