Deleting is not going to increase power by 60hp. You'll see an improvement, but not that much.
Factory exhaust is 4", but has a cat in the downpipe, then another cat, then the DPF and muffler...not pretty.
You're mistaken that any Holset or Mopar turbo is an increase over stock; Holset makes the turbo, a replacement turbo is the exact same as the factory turbo, and a Mopar turbo is just a Holset with a nice chunk of change added on to it.
Now, as far as the 5.9 manifold being more difficult, not so. True, there is an added expense buying a 5.9 manifold, but the easiest way to change the turbo is removing it and the manifold together, and you have the EGR cooler that might as well go bye-bye at the same time, so really you're going to have time involved in taking all that stuff off just to get to the turbo and manifold in order to remove them...
My recommendation, do the full EGR delete. If you want to keep the exhaust brake, get a factory replacement turbo. If not, get something in the ballpark of a 64/71 on a 3rd gen 5.9 manifold and throw a little tuning at it and the 6.7 will spool it just fine. Tuning? EFILive, hands down. It truly is the best thing since sliced bread. And an Edge Insight for a gauge pack; very nice unit, easy to use, easy to mount. I have the gauge pod from Edge in my 03 that has a 6.7 swap, and it's real nice.
Exhaust, you can spend around $300 all the way up to $7-800. That's completely up to you and what you want.
The best way to reduce EGT is to let it breath; exhaust and a turbo in this situation will be far better than water/meth. And Edge doesn't do DPF delete anymore, you would have to find an older used Edge race (and even at that, there are better options).