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Also, the rear is jacked up in order get the transmission and jack out. I went with my brother to BTS and I believe this is the main reason. When i did mine, I didn't level out the engine. Just dropped it and pulled it out. I'm lifted enough that I didn't have to jack mine up.
When I did mine, I put the entire truck up on jack stands just for more room, but the back wasn't up any more than the front, my engine sat fine. I do have a leveling kit on the truck, maybe that made the difference. And I took the tranny/t-case out as one, with a pair of floor jacks. Put it back in that way, too, I just found it to be easier that way since I was doing this solo.
Best advice I've seen here IMO is to get a u-joint and long enough socket extensions to get to the bellhousing from behind the t-case!
Putting a leveling kit would not make it any better, worse if anything. Think about it.
The reason for the bellowed pipes, is that it is a permanent solution to the daunting (even for an experienced mechanic) job, that you can do once, and fix it. The problem is that the two exhaust pipes connecting the exhaust manifolds to the turbocharger inlet collector use a compression fitting style ferrule, made of fiber and ceramic, to seal down on the pipe, when compressed. However, the pipe needs to expand and contract with heat, and over time, it wears grooves in the pipes, letting exhaust pressure leak by, hurting fuel mileage, efficiency and power. The bellowed pipes is a permanent solution, as it takes the same pipe concept, with a bellows connection welded to the outside of the pipe, and a positive contact steel gasket that does not move with heat.
When I did mine, I took out the front drive shaft. The bolts on the u-joint straps on the front have factory loktite and they have only 5/16 heads on them. I broke 3 sockets before I had to grind down an impact socket and heat them up. Heat them to begin with and they will come right out.