cold cylinders

[2500HD]

So i'll try to make this long story short and maybe one of ya'll can figure this out.
It all started with water in the oil this spring. I checked compression and found cylinder #6 to have no compression. I sent the head off and it tested bad so i installed new cylinder head and reassembled, retimed and got her running but kinda rough. I then felt the exhaust manifold at each cylinder and found #2 and #7 to be cold, so i replaced cap, rotor, plugs, coil and wires. No change. Pulled the fuel rail and the injectors looked like shit so i replaced those. Still no change. Checked injector pulse with a noid light and had pulse. Did a rudimentary check for spark by pulling the wire and putting an old spark plug in and starting the engine, seemed to have spark. also checked for color on both 2 and 6 and no color( all the other plugs are black like its running rich). Any ideas on what to check next? Could it possibly be fuel pressure affecting only these 2 cylinders. Would a bad ground do it? Or an ignition control module? I need some help here. I'm tired of chasing this gremlin.
Forgot to add that when i put a timing light on those cylinders it is very erratic.
Oh yea, the engine is a 2000 indmar 325 mpi
thanks