Post Engine Swap Intermittent Cyclinder Misfires
 

Have a 2000 S4 that I had to swap the long block due to damaged pistons in the crank and heads.
Found a APB long block engine that held good cold compression that came out of a 2001 A6 from a junk yard. Did the engine swap cleaning up things as I reassembled, etc. Didn't have to remove the heads from the new engine but bolted on everything else new with new gaskets, etc.
After putting everything back together, the engine fired up fine and after a few minutes was purring nicely.
Let the engine get to normal operating temperature and took it out for a road test. Everything went fine, until I stepped on it a little to put the engine under load and got misfires in cylinder 6 which quickly went away. A short while later got misfires in 6 again which then dominoed over to cylinders 2, 3, and 4. After about 15 - 30 seconds the misfires go away.

Troubleshooting steps:
1. Swapped coils from non-misfiring cylinders to misfiring ones.
2. Swapped spark plugs.
3. Shouldn't have been the ignition modules, but swapped them too.

With all the troubleshooting I've done, I still get intermittent misfires; always starts with cylinder 6 and sometimes will domino over to other cylinders.

The prevailing theories are:
1. There may be some sediment in the heads or crank from the engine sitting in a junk yard for about a year and it could take some miles for that sediment to burn off.
2. Perhaps some weird mojo from the injector off the manifold firing into cylinder 6? May need to add some injector cleaner?

The question for this forum is: Has anyone experienced intermittent misfires with one cylinder in the past that didn't seem to be spark plug, coil, or ignition module related and what ended up being the issue?

Thanks in advance for your thoughts / theories.

Here's the update to this issue (hopefully I'm not premature in posting a resolution; fingers crossed).

1. The plugs were actually gapped at .028. I regapped all of them to .032.
2. Ran the tank down to near empty and filled up with Chevron premium with Techron.
3. Added a bottle of complete fuel system cleaner.

So far (50 miles in) I haven't had any noticeable misfires. Hoping that the issue was spark plug gap related. I just have a hard time wrapping my head around the fact that being .004 closer to the electrode could make such a difference on cylinder 6.

Another suggestion that I have from a friend to help clean up the crankcase (since this long block did come from the junkyard and I'm not 100% confident on the prior owner's maintenance habits) is to add Seafoam before my next oil change.