Nathan:

The mistake was taking the engine apart when it didn't have anything wrong with it.

Not just the con rod, it wants to be in the original position due to the matching wear on the rod and the crank pin, but also the piston and liner wear one to match the other. You will never get them back in the exact position, they will have accelerated wear now until they reseat.

Just do your best to get it back as original, and hope the reseating doesn't take all the wear remaining in the piston and liner's life.

Bill.