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you do not raise the head you cut the dome on the piston or open up the head chamber if the valve hit they get bent and would run very bad retro roller cam hyd need retro push rods and retro lifters...

i would think it could be many things hard to say could be a wrist pin bushing or piston slap i would not say oh hell it is fine drive it ??as for a warranty good luck on that i back my machine work...

the pistons are hitting the heads ? valve hitting the pistons ?? you did not say what heads you have but if o ports with a closed chamber pistons like a old trw then they will hit on the EX side of...