Well, it was a royal hassel, but doing a clean install of the OS cleared up the font problems for me too. (I don't have Adobe Type Manager installed at all).
Don't know what was causing the problem to begin with. I'd like to find out, for curiosity sake if nothing else. I've done the 9.01 to 9.5 update on two other Mac G3's in our office and did not encounter the same problem.
CEA, thanks for blazing the trail ahead of me.