The 06 has gallery cooled pistons where the 03 is an SO design that is just splash on the bottom of the piston. The gallery cooled pistons are a better design and will take more heat. You might want to consider replacing the pistons in the 03 with the gallery cooled ones and make an HO out of it. The Cummins QSB pistons are the re-entrant bowl design that matches the 03 spray pattern and fueling curve and can be had fairly reasonable loaded with rings.

You would likely want the 06 rods as I think they are different for the gallery cooling. If you cylinder walls in the 03 are good I would pull the crank and rods from the 06 and install in the 03 with QSB pistons and the 06 head for best results. Make SURE you check the 06 rods with scored pistons walls to make sure there are no issues at the piston end.

Something took out the rod on the 03 and that was likely a bad injector, you will want new injectors also.