It makes it a lot easier if you had a spare running engine that you could bolt the carby onto this one to rule out a fuel supply problem and replacing an ignition coil from a good running motor helps as I've swapped coils from old motors and they still didn't work.
I take it when the valve clearance was adjusted the exhaust valve was fully open then the intake clearance was adjusted and when the intake valve was fully open the exhaust clearance was adjusted otherwise the clearances are wrong because of the automatic compression release mechanism.
Some of the carbs have a drilling that is vented to atmospheric pressure ( between the carb and head) and if people use the wrong gasket or install the gasket upside down it will effect how the motor runs.
If the motor is mechanically good (compression) and fuel and spark are good it should run well ,sounds like you have confirmed the mechanical side to be good unless the cam is worn out or a ring is stuck in the piston land or the cam timing is out and I would think you have already checked the mechanical side.
Valve guides can come loose and move and Valve seats can come loose.
