Update: I successfully installed one pipe this afternoon. In order to do this I had to grind on the up pipe enough to get the donut to fit. It was still relatively snug, I used the old collector (ears broke off while removing the old bolts) to beat it down on the pipe to where I thought it should be. Then I installed the new collector onto the turbo, then reinstalled the turbo onto the pedestal. Went underneath and stabbed the up pipe into the collector and attached it to the manifold. Using a long extension I installed both bolts into the collector and tightened them up back and forth to move the donut up the pipe until it was tight. This was much easier then trying to align the turbo to the semi mounted collector and up pipes. It was a squeeze to get the turbo and collector back onto the pedestal when they were already attached but not too bad. I dropped the bolts a couple of times because of the swivel on the end of the extensions but over all much easier and I feel confident that the donut is in the right place and didn't have to fight and guess where on the pipe it needed to be.
For some reason the donut was extremely tight on the pipe before the grinding. They are the originals but show no signs of wear so I didn't see the point in replacing them. At first I thought it was pieces of the original donut that was making it tight but I had to grind past that to make it fit. It was still plenty tight but lubed up the brass was able to move around. I don't know if it has sealed but hopefully tomorrow or Saturday morning I will finish and be able to tell, I will report back if anyone is interested.
On a side note I found out the EBPV had already been partially done by the previous owner installing the Banks Power Elbow. I gutted the pedestal because it was still original and was a source of at least one oil leak.