this is the top of engine with intake off. Valve covers are still on. My concern, and I am shooting from the hip, is that your variable valve timing is off, I would think it would throw a code. but sludge in the cam timing gear assembly could throw the cam timing off and maybe cause a missfire. I would remove the front valve cover which is easy to get to and rule out sludge. the next thought is unhook the battery for a couple of minutes to reset all codes in the main computer. It is possible the crank or cam timing sensors may be going bad, but I just dont know. Now your mechanic removed the manifold, I would be concerned that maybe one of the plugs to the fuel injectors on top might be loose or have some corrosion.... The second picture I have circled the injectors for the front bank. Both are accessable with the cosmetic cover removed....