If you haven't I'll post pics so you can see how much you need to grind.
"It seems as if the flange on the pipe wont clear the two allen screws that hold the flange that the pipe installs on"
I'm not sure what you are talking about here. The inlet pipe bolts directly to the turbo with 2 bolts. If you have allen head bolts those aren't stock and tend to have a much thicker head than a regular bolt. Even with regular bolts you have to pull the pipe away from the turbo in order to get enough clearance to start the bolt.