Same experience here, beat Tak but couldn't get near Bunta, haven't bothered trying as the gap seems huge.
Iirc you can transfer over to id2, but it's unlikely to be worth it. For a start the fd is no longer king of the hill in id2 and I also think your id1 save becomes unusable in the process...
I still haven't got round to putting any time into id2, I just seem to be busy busy atm with no time for games
