Need help, my mechanic is baffled

What is your question?

Brought my car in for a check engine light. Ended up having the intake manifold replaced. All codes went away, but one...the computer is showing a misfire in cylinders 1 and 4....everything is good, cam, compression, everything else. My mechanic is at this point baffled, and cannot figure out why....he says he's run every test possible...can anyone help??? He's had my car for 5 days