Well, that sucked. That may have been the most unhappy experience I've ever had under the hood. I have large forearms and big hands... that's not a place for a guy like me.
When I pulled the up-pipes, I noticed that the new gaskets were bigger that the pipe. I'd seen something about expanding them so I clamped a piece of tube in the vice, slid the up-pipe over and hammered the ends until they fit nice and snug in the collector. Hopefully help with future leaks.
Spraying the PB Blaster all week must have helped because I got all the bolts loose with no issues at all.
Here's the method I ended up using... (for anyone's reference who cares)
Pulled the intercooler pipes, spider, and down pipe. Used a ratchet wrench with a flex head to get at the back bolts. Used a stubby wrench to get at the bottom up-pipe bolts.
Once I got the up-pipes back into shape, I bolted them to the manifolds but left everything really loose, like not even finger tight.
Then I bolted the turbo up with the collector on the back. I bolted the flanges with the new donuts inside on the collector before I bolted the turbo back in and left those bolts really loose as well. Then I just wiggled stuff until both the up-pipes were in the flanges.
Then I went underneath and tightened up the up-pipe to manifold bolts with a stubby wrench. I had to use a 1/4 drive deep socket on the top bolt on the drivers side.
I tightened up the easy to access bolts with the flex end ratchet wrench and then got the ones hiding in the back from underneath the truck. I used a universal joint with a wrap of black tape like Arisley suggested and had that on a wobble extension. Then stuck a bunch more extentions together until I could reach those bolts from the bottom of the motor.
Made a huge difference. I didn't realize how much of a leak I had but now my truck is quieter and hopefully my mileage picks up a bit. I just used the Ford donuts, but if they go again (and I'm sure they will) a set up bellowed pipes are probably gonna have to happen.