matching the crankcase is probably the best thing you can do. just put the cylinder one one crankcase half and then align the ports between the cylinder and crankcase.
both my engines had a pretty bad overlap.
ive also cut down the cylinder skirt to allow a free path for air to travel from inlet to transfer port.
i bevelled up the cylinder transfer ports too (the ones in the base, dont touch the inside of the cylinder) but didnt bore them out too much. have to be careful not to stuff up the shape of the port as it directs flow to the back of the piston away from the exhaust port.
can also widen the exhaust port for some good gains too. just have to be careful that you dont widen it to the degree where the piston ring will catch and annihilate
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