Swapped Computer, now Fault Codes

So, I just put a used computer in my 98 XJ (computer from same year, A/T, 4.0L) and the Jeep runs fine, but I'm getting the codes 0700 and 1694 and then it says "misfire, O2 sensor"

0700: EATX Controller DTC Present This SBEC III or JTEC DTC indicates that the EATX or Asin controller has an active fault and has illuminated the MIL via a CCD (EATX) or SCI (Aisin) message. The specific fault must be acquired from the EATX via CCD or from the Aisin via ISO-9141.
1694: Fault In Companion Module No CCD/J1850 messages received from the powertrain control module-Aisin transmission.

Does anybody know what the causes of these are, or if maybe they are just popping up becuase the computer was swapped without reflashing it?

97/98 was a bit of a changeover year for the tranny computer. Perhaps you have some sort of mismatch? Is it a california model versus non-california model? Just curious, why'd you swap the computer?

I swapped computers because I fried my old one when I turned my Jeep into a submarine! I have another tranny control module that I pulled from the junkyard. I might try swapping that in and see if that does anything. As far as I know, the comp. is for a standard emission vehicle, which mine is.

Did you try disconnecting the battery after the first power up ? I know that there are some things that need the chrysler scan tool to set, vin, mileage, There might be some other settings in there. I'll be borrowing one sometime during the next couple of days to program another key fob for the ZJ and will hook it up to my XJ and just kinda wander thru the screens and see whats there. I know one of the interesting things between the 97 and 98 is the odometer, on the 97ZJ and the 97TJ's every time you select the trip odometer, shut the jeep off and then restart it it defaults back to total mileage vs the 98 that goes to the last setting. Mine is a aug 97 model, I'll see if there is some kind of 'about' choice on the menu to get some detail if I get the tool.

I didn't disconnect the battery afterwards. I'll try that. I did erase the codes with the scanner and they popped up again when I started it up next.