I've been working on the same thing with thesis.
Unfortunately thesis is using the 'root' paths for wp and not wpmu so there are some pretty serious hurdles to overcome to use it with mu. If I get it all situated out I will post the fix.
The biggest issue is exactly the same type of issue with timthumb.. The server is sending back image locations that to the script 'don't exist' meaning there should be a /blog_id/ folder in the url but there isn't.
this means that all auto thumbs are broken in thesis for wpmu.
I spoke to Kristella about this same issue and she sent me her solution, though I think I will try to modify it first. She is taking the approach of creating a blog dir inside the /custom folder for thesis to store the blogs individual custom.css and functions file.
I would prefer changing that to the /blog_dir/ folder for the individual blog. Same goes for the upload folder and cache folders for thesis.
I'm kinda hoping it's just a matter of hacking thesis to change the call for 'basepath' which it uses for wp to the 'basepath' for wpmu.
Still looking for documentation on that part.
Other than that.. thesis really rocks!
--maybe we'll get lucky and they'll be forced into a wpmu version very soon as it's more than rumored that wp and mu are 'merging' codebase.
Once that happens, than man life is going to be so much easier using mu.