Rich-
That stupid bracket thing does work great...if you've got a manual. Somebody at ATS didn't think of that when the designed this setup...
Any chance you could move the dipstick tube? If you unbolt it from the back of the head, maybe you can remove the upper half of the tube and "tweak" it a little to go around that bracket? Maybe you could cut a 1" section out of the bracket, and use some 1"x1/8" flat bar to make the bracket "jog" around the dipstick? I know that it's supposed to bolt in and doing all of this defeats the purpose of spending $800 on a kit, but we gotta figure out some reasonable way to make it work.
On your exhaust issues-
1. Did you install the exhaust while the truck was in the air on a lift? I did that with my MBRP exhaust, and it fit like **** too. Once down on the ground, that leaf spring compresses out of the way and the tail section can be slipped into the muffler a little more to clear the fuel tank and spring. I actually had to trim my tailpipe where it slips into the muffler to get it forward far enough. (this was expected, as my kit was designed to be "cut to fit" as it comes long enough for a 4 door longbed truck. I cut down to fit my supercab longbed...and mated it to my ATS downpipe.) EDIT NOTE: My exhaust still hits the spring and fuel tank when the truck is raised on the lift...but clears fine on the ground.
2. I ended up relocating the front most hanger (that bolts to the passenger side frame rail) back about 2.5 feet on my truck. Theres actually holes in the frame that allow it to just bolt on, but further back. With the clamp on hanger that goes around the exhaust piping, I was able to make it work pretty nicely. You should know: My exhaust is a 4" system designed for a 96-98 Powerstroke, so I had to do quite a bit of fab work to get it all to work. Your exhaust may be lots different...
3. When I had my truck on the lift today to change the oil, I looked at my setup again. I've got the exact same exhaust setup as you, but with a non-wastegated turbo. The slip fit up-pipe is leaking at the turbo inlet, but my downpipe seems to have sealed up after about 1k miles. My kit was used, so the up-pipe was pitted from rust a little, and fit loosely into the turbo inlet. The current plan is to use some 3M exhaust manifold sealant to seal up things. This 3M goop is supposedly used on racecars all the time, and is said to withstand constant 1500*F temps. Maybe a smear of that around the up-pipe before assembly will work for you as well.
Just trying to help...
Ryan