Hell, I have exactly the same problem. I have changed everything from the fan clutch to the differential and it still isn't gone. Engine is rebuilt and balanced, new balancer, flexplate is straight, converter is new and trans rebuilt, driveshaft is brand new. Vibrating as always. Next thing I'm going to buy is a new trans mount from Energy Suspension, a harder one made of poly urethane. If it turns out to have been that (or the engine mounts, which I shall also be changing), then I'm going to be really angry
Please keep me posted if you find out the source of vibrations, and I'll fill you in on any news I have.
Good luck,
Max