It shouldn't vibrate at all. Period!! I had my 360 balanced at my local speed shop and he required me to take in every piece of my rotating assembly or he wouldn't do the balancing. He told me if I changed anything consider the warranty null and void. I put it together and with a pretty nasty sounding cam you can set a glass of water on the air cleaner and it won't tip over it runs so smooth. It has absolutely no virations at any rpm's. Sorry to say but something don't sound right with the balance job you got.
And I don't believe it has anything to do with the mounts. The mounts do isolate the body from engine vibrations but the engine shouldn't be vibrating as bad as your describing.