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I will be running some ported and polished 799 heads with a valve job. my cam is a mti v1 cam 230/232 .592/.595 111lsa. Can I mill these down to 62cc and be safe or should I just run them stock?
Unfortunately hard to predict. You really need to know a lot more about the cam opening and closing ramps, intake centerline, etc. to figure it out. The minimum PTV usually occurs at approximately 10 degrees from the piston being at the top of the exhaust stroke when the exhaust valve is closing (piston chasing the valve) and the intake valve is opening (valve chasing the piston). Two things are working against you, the duration and the tight LSA. Unless you can find someone with that setup who can provide you their numbers, everything else would be a guess. Plan on measuring and determine the valve drop while the heads are off the car.
I have seen some people running the tsp torquer v2 milled down to 62cc with pariot 243 ported heads thats 232/234 .595/.598 112lsa. It's no big deal if not I may be selling these to get some tsp stg 2.5 5.3 heads anyway.
Depending on how heavily ported the chamber is...it might take only .010-.015" milling to achieve 62cc.
An alternative would be to use a .014" thinner head gasket ( .040" Cometic) to achieve about the same end compression ratio as the milling would get you if used with GM gaskets.
I think either way, you should be plenty fine with clearance, but if you were to do both (milling and Cometics), then checking actual clearance would be strongly suggested.