Computer reprogramming

So, I got the computer today that I had ordered. Plugged it in, the fuel pump primes like normal, jeep starts right up....but runs terrible. Totally misfiring, timing is definitely off. The computer I got is from a 2000, mine is a 98. I just found out that 2000 and later went to distributorless ignition. Does that mean this computer absolutely won't work on mine? Or can it be reflashed/reprogrammed? Anybody know a cheap place to do that? I called around briefly and it seems the going rate is $100 or so.