Bolt a cyl back on and itll be easy to determine the stroke size , if you got a micrometer. Just measure along inside cyl wall, bottom dead center, rotate crank to top dead center, should read 54mm of travel for stock , 58mm for 4mm , etc.
Long as the port timings are low enough and not too aggressive, should be able to have the cyls re-ported for 58 stroke. Or are you wanting to do this yourself?
You have access to any smaller carbs, that are setup for a ported,piped, possibly 4mm setup? I'm just curious if you got too much carb. Dune ported 4mm can run great on stock size/28mm pwks. Not sure if the extra timing is a handicap for too much fuel/air, just an idea.
I dont see 3* of timing advance fixing any carb issues, take the carbs off and thoroughly go through and make sure there good to go. Jetted correctly, etc.
Driveline has there stock looking head, that uses all common domes. But noss,chariot both make good heads, most sponsors on here will carry either. And should have pwk parts you need.