engine change out 94 gt 5.0

I recently changed out my tired old stock engine. with a rebuilt 98 explorer engine with gt 40 heads and intake and a modest cam. of coarse now the ECU doesn't know what to do with all the changes. would an ECU from an explorer help with my problems. oh yeh it's also has an AODE tranny?
 
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Are you still running stock MAF and injectors? How modest is a modest cam?

Based on what you described, the stock ECU shouldn't have too many issues (if you set TPS, idle and timing correct).