Regarding the MUI problem: There could be several causes.
Maybe the troubling applications use special mui classes that you must install first. Or maybe the screenmode you use is too small. It could be a missing library etc. etc.
As for workbench.library: The a4000T only used a special workbench.library with Os3.1. The a4000D and a1200 had workbench.library in ROM, but with the A4000T it couldn“t fit in rom, so with OS3.1 there was a special disk based version of workbench.library especially for the a4000t. With os3.5 and 3.9 all amigas use a diskbased version of workbench.library, so there is no special version anymore for the a4000t.