Welcome. This could be a number of things. I would start with a wellness check of the engine. Do a compression test. How does the engine run other than the vibration? Have you verified good spark on both cylinders? Maybe change spark plug caps as cheap insurance?
Was the clutch removed/disassembled during the engine work? Clutches are balanced and need to go back together the way they were from the factory or be rebalanced. This could cause vibes and also damage bearings/seals on the pto side.
A bad engine mount can cause vibes. Verify all mounts are in good condition and tight. Verify that the torque stop is set correctly. This is a small adjustable stop, usually in the area behind the primary clutch and keeps the engine from torquing/twisting too much. There is a spec but usually just get clutches aligned and all mounts torqued and run this up so it just touches the engine block and tighten the lock nut.
Good luck, keep us posted.