i always ran the 48.(not 49...only 49s are the pocket rocket motors, cylinder lies flat, reed valve block directly into crankcase from the rear...no good for pushies, IMHO...)
never had an issue.
the cylinder is angled maybe 5 degrees more forward than the larger 66. the cylinder is slightly smaller. as for cylinder height, think its exactly the same. maybe a few mm stumpier.
the dead giveaway is the size of the cylinder bolts. M6 on the 48, M8 on the bigger one.
is the vibration from the motor or the chain? always found it was the chain that did it for me on the most part.
make sure the engine is clamped up TIGHT. dont use rubber in between clamps and frame. using adaptors or anything increases vibration, the shorter and more solid the clamp to the frame, the better.
a large frame does soak a bit of the vibration up. long tubes. my lil vintage bmx/chopper frame did have more vibration than the 21" shogun. the engine only just squeezed in and needed a cj8 or similar "stumpy" plug, that was prone to arcing on the frame whenever it rained. the shogun had heaps of room(my avatar pic, 21" being the frame size, ie, the length of the seat tube)
never bothered trying a frame with fat tubes. i always just found standard 1" tubing frames to be easier to deal with.
its really hard to say just how much vibration is normal, anyways.
and, on the last thought...i always ran a tuned pipe, did fine doing probably 40-45mph. i hated the only 66cc that i got, by accident.
the pipe really helps on the vibration for some reason. that i can definitely vouch for. something to do with better combustion, iunno.
and yes, theres always sweet spots with ANY thing that rotates, be it a mower, bicycle or a highly balanced precision surface grinder spindle. its to do with the natural harmonics of a system coming into tune or resonance with any source of vibration.