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So once you have your cylinder to head distance (deck height) dialed in, you can then start looking at port timing. I would aim for at least a 150 degree exhaust port timing, about a 120 degree intake timing, and if you can get to the transfer ports and raise them without changing their angle(s), I would make them around 130 degrees. You want to raise the exhaust and transfer ports, and lower the intake port to get these numbers. Be careful when lowering the intake port that it doesn't become uncovered or open, when the piston is in the area of bottom dead center; effectively not closing completely. You can also widen the ports, but be careful when widening the exhaust port that it doesn't get so wide that the ring can bulge into the port when passing by. You can do all this porting with a Dremel tool and carbide cutters. Don't try to use grinding stones, as the aluminum will quickly clog the stone, and this can lead to the stone overheating and exploding. When you are done with the ports, be sure to give them a slight bevel to keep them from scuffing the piston or damaging the ring(s).

BTW, I don't recommend enlarging the ports without first getting the port timing set. A larger port won't help if the engine doesn't have the "time" to use the larger port.
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AV8TOR