Idk if the 49cc needs extra balance holes drilling in the crank? I have been advised that the no-name 66cc really needs them. Is your engine a Grubee or a no-name generic non-Grubee?
When the subject of drilling extra crank balancing holes was being discussed, I was advised to not attempt to split the case and remove the crank in case I knocked it out of true, and being ill equipped to retrue the crank.
A crank can be splayed, pinched or twisted at the big end pin where the two flywheels are joined. Some posts here have referred to these problems being present on brand new engines anyway.
I dont think there's a lot you can do about it if this is the case, but I would be checking by a very basic method, just touching something against the flywheels to see if the move it up and down when the crank is rotated by hand. Idk but this might show up if it's grossly out of true (?).
Also, (this is probably not the reason for the vibration, but) the lower end of the exhaust muffler should be supported to the frame so it doesn't snap the studs in the cylinder when the vibration shakes it.