I hesitated to post a reply, since I don't fool with Blue Oval stuff much. But, since noone else is trying I wiil.

Sounds like a lean surge to me. I had a 350 Chevy do that. If the carbs sat up without being cleaned, the jets may have varnished up. The power valve should not affect your cruise condition. I have 3x2 on my 46 so I know pulling the center carb can be a pain, but I would clean it out if you haven't done that.

As far as the timing issue goes, if any of the internals that affect timing have been replaced(cam,timing chain and gears) then the marks you made before tearing the engine down might not line up exactly. Manufacturing tolerences would be the culprit here. If the distributor is one tooth off, it could cause this also. I say let the motor tell you what it wants, if it runs better with more timing and doesn't have ping or detonation then run more timing(within reason of course).

Mike(who is in no way a FORD expert)