Hmm, asset builder shouldn't be causing any issues. However, with some versions of BfME you do need to create some base files before your new faction will show up it seems. Try that first, and it might help. The asset builder shouldn't need tweaking unless you're using all new graphics
!
Personally, I've never had any problems with ini file lengths - this is because I create new ini files for my content, and BfME is still able to load them.
Hope it helps,
AmberZ