Rod,
Whichever way you decide to shorten them, keep in mind that depending on the type of lock that your piston uses, you may have to be very careful to match the chamfer on the end of the pin. Spiral locks require a straight end with virtually no chamfer but a lot of the newer pistons use a round wire lock that depends on the chamfer to force the wire into its groove as the pin tries to move from side to side.
Of course if the pins are press fit into the rod, then none of this matters
