Hi,
I don't think there shouild be any problems with gasket thickness on carb case, Transmssion case or even cylinder base gaskets. The only thing you may have to do is reset the clutch lifter clearance if you fit a different thickness gasket on the transmission case joint (a thicker gasket will move the lifter away from teh clutch slightly).
The central crankcase gasket on the single cylinder bikes is slightly different, as it controls the end float of the crankshaft. There are some shims fitted as standard on the crankshaft - normally two each side. What I've done with my rebuillds is to do a dry assembly of the cases with the new gasket and just the crank in place with itrs original shims. Tighten the screws around the crank chamber. tap each end of the crank with a mallet to seat it and then try to rotate it by hand.
If the crank feels slightly stiff, open the case, remove one of the shims and try again.
If the crank feels free on first assembly, I raid my spares box and add another standard shim and see if the crank is still free. Keep trying that until the crank feels stiff, and then remove one shim.
Basically, the crank end float should be just less than one shim thickness.
Hope that helps!
Graham Weeks