rubber is definitely bad for motor mounts. you won't find one experienced builder who uses it.
the two biggest vibration causing things everyone overlooks is the gas tank and the exhaust.
and the gas tank is one place where rubber mounting actually helps!
the easiest thing to do is cut up an old innertube and wrap it around the top tube on the frame, then mount your tank on top of it. tighten it up so it doesn't move, but not so tight that the studs break and crack your tank.
the hanging exhaust pipe will also cause vibes, and without mounting it to the frame, either with the crappy strap the kit comes with, or some plumber's pipe strap, or whatever you can come up with, it'll vibrate, come loose, and break or strip the studs in the engine.
a simple test which i've mentioned many, many times, is lean your knee into the tank when the vibes start. you should feel them decrease or go away.
you can also put your foot against the exhaust pipe for the same type of test, if you don't mind losing a little shoe rubber...
any loose parts will cause vibrations. some minor, some serious.
and if your bike ever suddenly starts vibrating when it never did before, something's usually broken. like your frame. happened to me...