Yes it should as they would reflash it to your vin and just load a 5.9 Tune

 

I decided to stay with a 5.2 to make it all easier, although I have another question. What would the biggest cam I could use without replacing the push rods/lifters/rockers be?

Its just gonna be a strict mud truck, might take it to work every now and then, but mostly will be used in the mud.

 

Max lift on stock valvetrain is .480. I would give a little bit of space there as well. Coil bind is not your friend.