Broken TB @ 140K miles... makes me wonder what other TDI specific maintenence was ignored...
Without pulling the head to check for cylinder & piston damage, it's hard to say... John's $500 offer would be a low-ball number... since if all it needs is a rebuit head it could be fixed and resold for a tidy profit, but if it needs a long-block, much less so. Pull the glow-plugs and video-scope it.
MkIV TDI's have 5 spds. 6 Spd conversions have been done, but they're pricey. Auto-manual conversions are a bit pricey as well... and tedious. And given this car's questionable history, I'd fix it and sell it... preferably to someone on the other side of the country...