Depends upon whether you are using J pipes or 4 into 4's. With 4 into 4's, you have to install the side pipes and then determine (1) the "levelness" of the pipes, (2) the distance from the ground on each side, and (3) the relationship of the pipe to the frame, ie are they parallel. There is a different adjustment method for each problem. After all those parameters are set, then you can install the hangers. You can't adjust by moving the hanger placement. With the J pipes, the whole setup is much different, and I'll let someone who has used them tell you how to do it. If you want more info on the 4 into 4 setup, I'll be happy to give you a step-by-step.
I elongated the flange holes which gave me about 10 degrees of adjustability. No leaks using hi-temp silicone only. I used that method to get the pipes parallel to the frame (and the ground) in a vertical plane. You may also find the need for a shim or 2 under either motor mount to get both pipes an equal distance from the ground. Finally, you may need to loosen the transmount bolts and swing it left or right a little bit to get the pipes parallel to the frame in the horizontal plane. I must admit, my headers and pipes fit pretty damn good, and I only found it necessary to elongate the holes on the left side.
IMO the best way is to fit your sidepipes only after the body and doors are completly assembled ( windshield,interior mirror,and doors are installed and have been and adjusted to they're final postions).With my car I had to use spacers between the body and the body mounts along the side of the car,this I did after cutting and welding my exhaust to get the pipes level and parallel to the frame,well after installing the spacers my body was no longer parallel to the frame,this caused the gap between the body and the pipes to narrow at the back,which required me to cut and weld the pipes a second time.Morale of the story fit the body and doors before the exhaust.
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