You can drop the floor of the exhause carefully using a file so you can get alignment, or you can drop the cylinder a little with a thinner shim and slightly ramp the periphery of the piston crown at the transfers. Keep in mind that the two base gaskets you now need will have volume and also will compress, good practice is to have 4 tubes on the cylinder studs so you can torque the nuts onto the assembly while you index the cylinder.
If you do decide to ramp the crown, just be wary of the margin over the rings at the exhause. You do not want to take it down too far because the reversion wave from the expansion chamber will be blasting charge back into the cylinder. If it is knife edged then that area or the periphery can erode quickly.