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

[cadunkle]

What are your compression readings before and after the top end rebuild?

[2500HD]

before rebuild they were all in the 137 to 142 range except cylinder 6 which was 45. after rebuild they are all 137 to 143.

[2500HD]

#2 and #7 haven't changed. they are my cold cylinders. Also the boat has always had a hesitation on take off that i am now blaming on these 2 cylinders.

[Moor]

Its either fuel or spark thats not getting to the 2 cold cylinders, and you said your getting spark with the rudimentary spark test. Were the two bad plugs wet with unburnt fuel when you checked their color? Also double check your spark plug wires/firing order. Its easy to mix up 2 wires, and that would explain your symptoms. If you have good injector pulse on the noid light i doubt its a bad ground, especially if its only on 2 cylinders. I'm guessing its ignition related, since your getting erratic reading from the timing light on the 2 cylinders.

[2500HD]

Update! Boat runs great, apparently i was a moron and used a plug wiring diagram off the internet instead of using my brain and following the 18436572 firing order around the distributor. God i hate moments of stupid.

[docdrs]

Thanks for the update, glad you found the culprit

[CornRickey]

when you have several things going sometimes its hard to pinpoint issues

[Moor]

glad your smooth running again 2500HD, and it was a free fix!

[CJD]

18436527??...if it was on the internet it must be true!