However there are still some problems/bugs that I couldn't find in your list to fix.
First of all there is that VERY annoying respawn-and-switch-weapon problem. I always have to use the starting weapon once, before I can switch to another one. Especially when starting with a heavy weapon this is totally annoying. Some weapons are even "invisble" before shooting them once (I've seen that happening with the 8-Ball and the Vulcan-Cannon).
Another bug, which is minor though, is happening when using the inventor-gun. If you do not press alt-fire you can always spawn a Tomahawk, even if no Soldier is in your team.
Another thing (has already been posted here by someone) is that somehow U4eF does not allow bonuspack models. I have no mutators in use with U4eF. I've tried it several times, but no matter how I set the "force Default Models" option the game always uses standard models - sometimes even with weird looking skins (ever seen a Skaarj skin on a human body? maybe it was Hannibal Lector...). Someone responded to the original post that it is a problem of UT, but I don't think so, as I never had a problem except the mod wanted it so (don't remember the names but I had two mods that wanted default models because of "fairness"). I have only tested it with the bonuspack models (Nali, Warcow, Skaarj Hybrid, Xan-MK II and Warboss) of which noone did work. I don't know if real custom models work.
A final note: Please enhance the sounds of U4e (not for 1.1, but this HAS to be done)! The sounds are the weakest point of U4e. Okay, some sound great (King of Funk), but others don't make you feel what you have in your hands (especially the AK-47 and the M16)