[mthused]

I owned and put 160000+ miles on a 1999 328is manual. It was an excellent car and felt very 'right' to drive. Lots of common issues with these but nothing too terrible in most cases. Interior pieces tend to be fragile and deteriorate easily (door cards, headliner, etc) aside from the other issues mentioned.

Clunking in the center might be the rubber flex disk between the transmission/driveshaft, or possibly the driveshaft center bearing? The flex disk is pretty easy to replace. Could also be the rear shock mounts- those also go bad pretty regularly, but the clunk is from the rear with those.

EDIT: One other possibility for the clunk is transmission mounts- all the rubber parts I'm sure are dead if they haven't been replaced...

I think it would be a really fun project car to share with your son. The M52 engine is pretty bulletproof aside from the known cooling system issues.