I can only speak toward my experience on parts/availability as it goes for the 6.0L:
- Everyone and their grandmother claim that a 6.0L with NV4500 exists on every street corner. In reality, since I started my swap over 8 years ago, not a single person has been able to provide me with a VIN for one. EVER. Thus, no factory tune is available.
- I went with aftermarket tune that I'm not happy with. FWIW, an auto tune is VERY different than a manual tune. I don't recall if it was spark tables or fuel mapping tables but you will NOT get an auto tune to run a manual. YES, I tried.
- If I recall correctly, except for the early GM NV4500(to 95???), they used an internal slave cylinder that many don't like.
- The early GM NV4500 used an external slave that was on the passenger side. The bellhousings between early GM and EVERYTHING else is NOT interchangable. I found this out first hand when I ordered Advanced Adapter bellhousing and clutch parts. While it is possible to get clutch parts individually, I've seen so many different parts lists, I have no confidence in any of them. AA parts were a bit more but at least I know they were correct.
- I believe AA adapters require 4wd NV4500 whether it is GM or Dodge. A split case is NOT required but I went that route because I don't trust the strength of the older 1 piece.
- For the oilpan, you don't have to do anything but I would recommend an H3 pan and NEVER touch a F body/Camaro pan. People want arm and leg for F body/Camaro pan even used($200+). You want the following pan ( I paid $150 a pan a year ago): Amazon.com: GM Performance Parts 19212593 Oil Pan: Automotive
I've used the above part on two LSx engines. It is complete and nice. NOTE: it requires use of 2005ish or later oil filters no matter the donor engine. I bought a case a filters for a 2004 6.0L that don't work with it
For ebrake, I went with new axles

Not much help, but there it is.