four mm shouldn't change it too much, its just simple geometry and the hypotenuse changing 4mm wont really alter the major leg much. probably 2 mm at most. What is the current stroke? Did you port for the longer stroke, or leave stock porting? Is the piston coming to the bottom of the ex port now, as in, did you calculate all that spacer-stroke-rod mumbojumbo correctly?
i'd be looking at something else if it were me.. reeds? 'speed holes'? ... hmmm
at this point, make your own crank, do a little heat treating or case hardening with some mild steel and call it a day, or get radical with tool steel.... or, or, or
i still dont see how you used that cylinder with 50mm stroke and didn't modify exhaust... wouldn't you have to lower exhaust port to make it even with the piston at BDC.. i mean, ideally at least?