[Marshall V. Daut]

My #1 reply in such cases is that the ring gear has worked forward on the flywheel. But you seem confident that it is seated all the way around. Scratch that one off the list. Maybe.
My #2 suggestion, then, agrees with Tom Endy: flywheel bolt heads being clipped by the inner hub of the clutch disk. This actually happened to me 17 years ago with a freshly rebuilt engine. The flywheel had been resurfaced and when it came time to mount it to the crankshaft, where, o where were the four special bolts required to secure the flywheel to the crankshaft? The gremlins got 'em! I had four new repo bolts I was saving for a customer's engine, but it was the weekend and I needed my engine running by Sunday. HIS new repo bolts were installed and the drive train was finished up by Saturday evening, just in time for a quick start up and check. The engine started fine and seemed o.k. - until I pushed in the clutch pedal. "Clunk, clunk, clunk!" Release the clutch pedal and noise stopped. Push it in again: "Clunk, clunk, clunk!" I am anal about mounting the ring gear squarely on the flywheel and even staking it in place, so I knew that was not the problem. After checking everything else out and finding nothing askew, I resigned myself to removing the transmission/bellhousing and pulling apart the clutch area to find the problem. Cutting to the chase, sure enough! There were shiny scraping marks on the heads of those new repo crankshaft bolt heads. Apparently because the flywheel had been resurfaced (i.e., made the center section thinner), that moved the clutch disk just that much closer to the bolts. After more scrounging around in my garage, I was able to dredge up one original crankshaft bolt. Comparing the repo bolt head against the original one, the repo bolt head was almost 1/3 thicker. Teamed up with the clutch disk being moved closer to the crankshaft flange during resurfacing, that was all it took to put the disk in contact with the thicker bolt heads. Pushing in the clutch pedal made the clutch disk hub flex enough to do that. I ground down the four bolt heads enough to reduce their height, while saving enough "meat" for the safety wire holes. Putting the whole mess back together again resulted in NO knocking when the clutch pedal was pushed in. Dressing down the bolt heads was the ONLY thing I had done stop the knocking.
Long story just to suggest checking the bolt head thickness, but I was trying to document what I went through to solve the problem. ^%#%& reproduction parts! Why can't a simple thing like a bolt be manufactured correctly??? Jeez, Louise!!!
One other thing to consider that I discovered just this year. Not all clutch disks are created equal. Some have a thicker center hub area than others. I discovered this in a friend's Model A that clunked when the clutch pedal was depressed. It actually stopped the engine with a BANG!! Removing the clutch disk and comparing it to one purchased from a parts vendor, it became apparent that the one I had installed out of my "parts bin" had a thicker center hub than the Model A vendor's hub. And, no - I didn't install the disk backwards. It's almost impossible to do that because you won't be able to bolt the pressure plate cleanly in the flywheel recess. The disk I used was clearly meant for some other application, even though its dimensions otherwise were correct. When you pull your clutch to fix the problem, be sure to compare your disk's center hub thickness to a known good disk. Be concerned only with the side facing the crankshaft.
So, there you are! Two possibilities to solve your problem: crankshaft bolts and clutch hub thickness. If you are POSITIVE it's not the ring gear (and your symptoms do point in that direction), I'll bet it's one or both of those animals at fault.
Marshall