I bought his Stage 1, comes with the manifolds and hot side (up pipes and t3/t4 mount). You basically do the same thing you would do with any of the other kits on the passenger side - remove the pinch weld. With that done, Mine fit fine and that included the up pipes being wrapped with header wrap. I have a ZF5 so I am not sure about any other tranny issues. An ATS 088 was on the truck originally. I do not have a body lift, and my cold side is a full on 60-1 housing, backing plate, and wheel and I don't have any fitment issues.
Unless you plan on moving the engine in and out a few times, it's MUCH better to buy his kit. All that work is done. There is no way to use the stock passenger side header, or easily use it, with a manual. The slave cylinder would be right in the way and probably melt lol. That being said, I use mine as a daily driver so I had to move more quickly and went with a kit where this was all figured out for me and I had just had my turbo rebuilt so it really made sense for the $1,200. If it is just a project, go for trying to do it yourself. Just takes a lot of effort in my opinion.
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