The problem is that it's not really "right " when the cylinder is for a 72mm stroke. I am not an expert but I will tell u I am one of the guys who has a 330 4 mil stroke and the cumbustion chamber shape is a poor design when the piston comes over deck height 2mm. In talking with other builders that seems to b a part of my overheating. This motor has never been right from the first time it was started. Bought all new esr cases, cylinder, Carb,pipe as a package and a hot rod Crank I sent to Crank works to have balanced and welded. Wasn't used Parts. Set up by Eddie for the stroke. And I have not rode it more than break in time. It has been a basket case . Several builders claim it's the stroker causing problems.
I am sorry but it sounds like you are another victim of the stroker crank industry and the mystique they have created. Do not feel alone, I have seen similar engine messes like you described and heard similar stories to yours hundreds of times. Builders that really know their stuff and do a lot of development with pipes and cylinders, do not usually have to resort to using stroker cranks to find the power they are looking for. Reliable engines with low end power, a wide power band and some serious peak power can be obtained when enough development time is devoted developing a good engine package.
My experience has been that adding a lot of displacement to an existing engine design is a short cut and cheap alternative to gain power with many undesirable consequences. Customers and builders that use and believe the old phrase...there is no replacement for displacement..... are admitting their limited knowledge on the phenomena that occurs inside engines and how making just one small change, affects the engine as a whole.
The stroker crank is not what is causing your problem. The problem is the wrong components and modifications were performed trying to use components that were not really designed to work with the stroke you or your engine builder selected.