Hi
If the bike has had the vibration since you have had it,it might be a simple as the crankshaft not in balance ,the early crankshafts are full circle flywheels, the later model "pork chop" crank rev faster but are a bit lighter, the combination of aftermarket pistons, the wrong model ignition flywheel , is possible , also if it has been assembled roughly , hammered together without heating the cases, it may have altered the "alignment" of the crankshaft cheeks.
A lot of CZ internals are the "same" ,that is they will fill the hole , but its the combination of those bits from the other different models that make for better motors