[scooder]

I think its internal engine vibration, its gona have to be pulled again and fixed. Clutch aint the problem in my opinion. I work on a massive aray of classic cars, have replaced lots of clutch's in my time. Not one of the replacement's required it to be balanced with the flywheel. When you fit a replacment clutch and the flywheel is in good order, you simply bolt the clutch on the flywheel, and away you go. The clutch assembly should be in balance out of the box, and if it is, it dont matter if you clock it at each of the three possible angles (long style clutch, used for instance) it should not/wont effect the balance of the engine.
Your vibration sounds to me to be as I said, internal. Crank,rods.pistons need to be ballanced.
I highly recomend you take up one of the earlyer offers from highly skilled Flathead mechanics, for a rebuild.
Get it done properly, you would have been clicking away miles on your odometer, with a silky smooth engine, instead of the pain of having to do it again.
Sorry if it sounds like a telling off at the end. But thats the truth.
Good luck.
Martin.
Just read the above post, I agree any decent engine builder should be able to do the work, Balancing and machining, rod rebuilding, maybe not the setting of the floating bearings if not done before. Though he could do a bit of research and then do it. But all the rest, no problem.