As they mentioned you'll want to get the transmission built first. You need more air and more fuel to make more power and you'll run out of air before you run out of fuel.
You are going to need a larger charger something in the 64-66mm range. I would step up to a T4, but if you stay with a T3 you can use your stock manifold. Aftermarket will flow better, but it depends on your budget.
Smarty seem to be pretty popular tuning for the 5.9's.
Don't waste your money on intake horns, boost tubes and what not. I would also get a set of head studs, it's cheap insurance to keep your head planted. Once you start running out of fuel then start upgrading hard parts. CP3, lift pump and injectors/tips etc.