The EGR will come off with the intake and replacing it at that point is, as they say in Boston, "wicked easy."
To put the delete in, just connect the rubber hose where the other one was, then just slide the u-pipe into the other end. The end of the egr delete pipe that has an o-ring on it pushes into the bottom of the intake. How that is held into place depends on the kit you purchased, but I believe that there will be a flat oval piece of aluminum that is slotted and has 2 drilled/tapped holes in it. The slot cut out of that piece goes around the u-pipe you just installed into the intake, the gasket side of that aluminum piece goes toward the intake. The two bolts come in from the top of the intake near where the EGR valve is. Thread those through the aluminum piece. Your done installing your EGR delete, except for installing the new up-pipe.
When you do this step, I will caution you that there is a metal gasket between the y-pipe that comes off the turbo and the new pipe you are going to install. Don't forget to put that in there. It will leak if you don't, don't ask how I know this.
Tighten the two bolts that hold your new up-pipe to the y-pipe.
LOOSELY install two bolts through the exhaust manifold on the passenger side.
Finish all the other stuff as far as re-installing the intake from you oil cooler replacement.
Place the turbo on its pedestal, DO NOT put the turbo-to-pedestal bolts in yet.
Do not even hang the down-pipe on the turbo if you can help it. (big exhaust downpipe off the turbo, not the y-pipe)
Have the marmon clamp hanging on the back of the turbo, but NOT on the inlet flange (inlet is where the y-pipe attaches).
You MUST get the y-pipe-to-turbo connection PERFECTLY aligned before putting the marmon clamp on. Don't let the y-pipe move as you install the marmon clamp. Believe it or not this step will probably be as difficult as anything else you do with this whole job. Being careful and methodical in this step will save you from having to take it all apart again when it leaks, and it will if not installed properly. The marmon clamp is designed to hold the connection together and it will NOT pull the pipes together if misaligned. If you are not careful and do not do this step carefully, you not only risk having to take it all apart to fix it, you may also stretch the expansion joints on your y-pipe. Do that and you will have to take it apart again and replace the y-pipe. Again, don't ask me how I know this......
Once the y-pipe is on correctly, tighten the bolts on the manifold end of the pipe, install the turbo bolts and everything else, properly torque each bolt to spec, of course.
A short list of stuff that, if you haven't done them, you might as well do them now since it is apart:
Updated turbo oil drain tube
updated turbo oil supply line (no longer has the stainless steel section)
updated fuel pressure spring (it will be easy to get to now)
If you are contemplating installing the banjo bolts from the 6.4, now would be a little easier
Do you know which STC fitting you have? Known for failure if it is the stocker (05-06 trucks). Theres one available at Ford that you should SERIOUSLY consider installing. It has a bracket that holds the connection and gets rid of the STC style fitting. Do that and you will NEVER worry about that fitting again. Its short money and install isn't too bad since your in that deep already.
Sorry for getting long winded, and you might have known most of this, but someone else may need this info.