PCM is different but people sell tunes for it...it just has a little "chip" you have to transfer over basically.
Cowl design for a cabin filter? You nancy. Breathe the crappy air. Also, '97-'98 and even seen some '99's with the coolant bottle by the air box, I actually like it better there because you don't have the chance of eating through your burb tank with your belts. So, like I said...only thing I'd worry about is the transmission.