Wow. Sounds like there is a bird caught in there somewhere!
Only time I have encountered anything similar was with a 150,000 mile fan clutch, that would would lock up intermittantly....but you eliminated that kind of issue long ago.
I think you're looking the right place (stem to guide)
As a union trained master mechanic/machinist, tool and die maker with 30 years experience explained to me:
As a general rule of thumb, .0008" is a magic number as far as normal human, layman capability to "feel" clearance goes.
Clean, lightly lubed, near room temp, a wrist pin or a valve will usually fall through the hole under it's own weight at .0008".
If it wiggles, either it's looser than .0008" and/or the parts have an irregular shape (not straight/round).
If you have to push it through the hole with any pressure, it's going to be tighter than .0008" and/or the parts have an irregular shape (not straight/round).
That might sound silly but I have put it to the test, and have found it to always be correct.
I believe you're going to find the actual clearance is .0007, 7 ten thousandths of an inch or smaller.
Personally I want .001 to .0025-ish stem to guide for most street apps
To me, tight guides are an accident waiting to happen (what happens when a valve sticks open?) and could cost you an engine
