Sn1perdeath

Hi everyone. Hope someone can help me with this one. I have a 2002 Civic coupe, 1. 7 engine, manual tranny. Recently had engine replaced and although it works well, it now has a "flickering" engine light. It seems to do it more under acceleration. It isn't flashing, just flickering. After 2 days it's an annoyance. No visible engine misses or any kind of problems. It had codes when it came back but after clearing them they haven't re appeared. P1106 BARO Sensor Range Performance Problem, P0108 MAP Sensor Circuit High Voltage, P0116 ECT Sensor Range/Performance Problem.
I assumed it was from having sensors unplugged at initial startup since there were no issues with the way it is running. Correct me if I'm wrong and please help me figure this out.