It's hard to mess up on a diesel as far as leaning it out. You start with a small jet and work your way up, when it starts losing power, back down a size or two and you're good to go. All you really want to do is clean up the fuel that's already there. We use dry systems too, not wet systems like a lot of gas cars. We've already got the fuel, just need the air to clean it up.
Rods are good to about 700-800hp on these from what it seems, at least reliably. They've been pushed to more, but I wouldn't' count on them lasting.
Regardless, it's not a necessity for your build. You'll like the SCT, it should already be a big improvement.