331 stroker build

Will this set up work ok for piston to valve clearance? Any recommendations are appreciated.
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Well no one can say for sure because you have not said what ratio rocker arms and even then you won’t know for sure because you need to know head gasket thickness and if the pitons will be below, even or above the deck of the block at TDC. If it was me I would get a custom cam but that’s me.

Those heads are not ideal of a 331. Again not sure what kind of power you want or if it will be NA, boosted, or on the bottle. Depending on that I would probably go with a minimum of an AFR Enforcer 185 or a TW 11R 190. I have the heads you want to put on however they have had port work and flow a lot more than stock. Got the heads cheap so it made sense.
 
Small heads and wrong cam for a 331. 331's like to rev,mine pulls to 6500rpm with an F cam. I actually ran those heads on my 331 1st,because I already had them. Along with a Lunati cam the car ripped. What is your intended goal with the car?