Was that with a warm engine or cold engine?
Did you get the pistons back in the same cylinders?
Was there a "ridge" at the top of the cylinders? (If there was, did you remove it?)
What HG's did you use?
It dosen't really sound like a rod/main bearing to me. They usually get worse under load though.
Also, usually a rod/bearing going bad will trip a "knock CEL", P0463.