Where does the extra rod length go? Say you're running a stock stroke with a stock 6.100" rod (technicall 6.098.) Then, you move up to a 6.125" rod... where does that stock length go? Does the piston come out of the deck an extra .025", or do you buy pistons with the wrist pins moved .025" higher in the piston, or is the crank lowered .025" by different bearings or machining??

 

You buy a piston with a smaller compression height to account for the length rod your running. You should try to run the longest rod you can do reduce the side loading angle.

 

Usually when you order pistons theyll ask the length of the rods to that you get pistons that have the wrist pins located higher up.