Engine replacement problems with 97 Exlporer

I have a 97 Explorer 4.0L SOHC 2wd engine that I replaced with a 98 Explorer 4x4 engine. It's running fine but the check engine light shows all kinds of codes for the transmission. The Overdrive light keeps
blinking as well. I'm wondering if I need to recalibrate the computer to adjust for the different engine type.
Has anybody experienced this problem ? Where can I go to get more info on this matter?
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You're using the same PCM... and it's not showing engine, but transmission codes?!!
sounds like wiring problems
ford-trucks.com forums might have someone who's done the same ..
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