that is a super thick base gasket. that would mean you dome step is nearly nonexistant.
your jetting is off. its that simple OR you have a synch problem, fuel supply problem, or ignition issue.
you need to concentrate more on the off idle performance get the bike to roll on very nicely and run a really rich main till it does that. then check stuff like spark gap, plug resistance, ignition pickup gap, plug cap resistance and you will need massive fuel delivery to enable you to run much high rpm for very long. including most likely another power jet added. you will have to watch your egt's if you make very long runs as they will continue to rise rapidly.
52-58 squish clearance is fine DO NOT tighten it up infact going to about 60tho may be even better for really long runs.
i would also highly suggest putting the PV's back in it.