Thanks for the advice guys. This is the exact one I ended up buying, didn't see this until after I bought it -
http://www.fordraptorforum.com/f24/twin-turbo-ford-raptor-here-29506/
It's been an interesting few weeks owning my raptor. A week after I bought it we had some snow and I put it in 4WD and the trans case shifted but the front wheels did not work... Well, a few hours later and a few choice words I figured out that the vacuum lines on the solenoid for the 4WD system were backwards and it was always providing vacuum so the front actuators never engaged. Easy change, just can't believe it had been that way since I'm assuming it was turboed a few years ago. Swapped the lines and worked like it should.
A couple days go by and I get home one day and notice the turbo oil pump isn't running when I parked. Pop the hood and there is lots of oil that had came out of the BOV. A wire for the pump had come undone and it turned off while driving. So the whole intake system was now full of oil, so I re-hooked up the wires and took everything apart to clean. Luckily the seals on the turbos look fine and haven't had oil problems in the intake since. I also decided to replace the pump with a new exapump because the gears were making a ton of noise.
So back to the original issue, I've checked all the basics and replaced all the plugs. A few were carbon fouled but not bad. I decided to replace with some different NGK Iridium plugs as i've seen lots of people/kits used them for forced induction setups on their raptors. Plugs weren't the issue, still have the hesitation.
One thing I was surprised about is there was no boost gauge installed at all, so I put one in so I can see the read out now. I was told it was tuned at around 4-5 PSI, but now I can see that. I do have some surging in pressure/vacuum when accelerating @ probably 75%, but at WOT it does not surge. The hesitation issue persists at 1.5k - 3k under load.
Today I just started taking a look at the data logging, new to doing this so It'll be a learning experience. Any advice on what to log or resources to look at? Anyone in here done a lot of data logging on their raptor before? I have an SCT X3 tuner.
I'd like to diagnose the issue myself, but if it comes down to it I might just have to take it somewhere around here...