Just because the valves have been shimmed to the correct clearance does not mean that they are sealing. Doing a shim job more than a couple of times indicates that the intake valves are sinking into the valve seats are not sealing. In most cases the exhaust valves wear the valve guides and then do not seat.
Unless you have had a recent valve job done I would consider that to be the issue.
Also a worn cam chain will cause issues as well.
RE: Flywheel...Photos would help.....
Also as already stated the pilot jet may be dirty or clogged.
Paw Paw