Many of these trucks came with the wiring for remote start. On some (like mine) you need to buy a new hood latch as there is a safety that disables the remote start from activating when the hood is up. (or you can bypass it with a jumper.)
I doubt whether any warranty or recall work will be done on a deleted truck. Take it to a transmission shop as they will have experience pulling the tranny that is required to access the tone ring and CPS.
Talk to EcoDieselCanada for a tried and true thorough kit.
You could consider a tune from Green Diesel Engineering also.
Be very careful because it is very difficult to unscramble an egg. There are many "tuners" out there but only a few reputable ones.