The fuel rails need to be swapped unless your crate 6.2 comes with them. When the Gev V 5.3 (L83) is built to make more than 500 horses, all the tuners and build shops say you need fuel rails off a 6.2.
As others have stated, VVT, AFM, DOD are part of the Gen V LT motors both 5.3 & 6.2. You can turn them off with a tune. The 6.2 should bolt right up to a 6L80. On the new trans you need to invert the thermostatic valve so it doesn't restrict the fluid flow. It will keep the trans running cooler and greatly increase trans life. Also you want to change that trans fluid and filter every 20-30k