Intake manifold causing p0174?

The infamous intake manifold finally crapped out on me (the thermostat housing broke) so I got an improved one from a lincoln navigator, first thing I noticed when I took off the old one is that the area around cylinder 1 has pits and corrosion, I paid it no mind and put the other intake on, well sure enough got some misfires and rough idle so I took it off and noticed the gaskets do not align correctly, but the holes themselves cover the cylinder heads so I used some liquid gasket (too fill the pits as well) and it runs much better, but still has a cylinder 5 misfire (the cylinder with the pitts) and shows bank 2 is lean, the pits in the cylinder head are most likely from coolant corrosion and the deepest one is about an 1/8th of an inch so any thoughts? is machining the heads possible? should I replace them and if so do they both have to be the exact same ones? or do you think the intake manifold is still the root of the problem? I can't get a good test using starting fluid being as if it is an intake leak it is on the inside making getting fluid down their impossible, been stuck on this for 4 weeks now, any thoughts would be appreciated.