Blacklight98

I am having trouble with my check engine light not cooperating after a manual trans swap. Looking for any assistance on what to do with the ECM to make it functional. I pulled the manual trans from a 97 R50 and put it in a 98 R50. The ECM plugs are different between the two vehicles. Has anyone ever had this issue? If so what is the fix? My plan is to build it into a very capable off road rig but I will need it to pass state emissions first.