Well, After all is said and done it was my turbo that Finally was the culprit and having it rebuilt fixed my limp mode.
I'll list everything I found that needed attention and/or replaced on my Rig which had 149,000 miles on it when this all arose
If you read this far you should know the sypmtons i was having.
1st--replaced Filter head due to it leaking @ the fuel heater Plug(did not resolve the issue)
2nd--Once the new Filter head didn't resolve the issue, I took the advice of papindigo and did the timing belt/Water pump. This needed to be done and I had put it off long enough.(Wasn't planning on this to resolve the problem just maintence)
3rd--replaced the Boost Hoses w/ Samco's due to tear in one of the originals, noticed while doing the Timing Belt(did not resolve the issue)
4th--sent ECU in to GDE & Weeks101 EGR Delete thinking possible EGR issues(did not resolve the issue).
5th--replaced the boost modulator, solenoid, and Map Sensor to make sure none where the culprit(still the same issue). I had done the Boost sensor Bypass and it still went to limp But all of these sensors were under $80 together and figured it couldn't hurt.
At this point I figured it was most likely the Turbo or the Tranny that was causing the issue.
6th--installed a boost/EGT gauges. At this point I wanted to see what was going on with the Boost when it went into Limp Mode. As far as I could tell the boost seemed fine, now while I was installing the EGT Gauge I took off the exhaust pipe and moved the fins and it seemed to be fine as well. I even moved the vane actuator by hand up and down a couple times to see if it stuck, it was hard to lift up but moved a good amount(the 1/2" that is mentioned earlier). But once everything was back together I couldn't get it to go into limp mode. Figured I possibly moved actuator enough that I broke the vanes free. Everything was working for a day or two.
7th--While it was running good, I took it in to a Tranny shop to have the tranny looked over, possibly find a deep code and have the shudder addressed. No codes in the tranny module but the shudder was addressed and I have a rebuilt tranny with the upgrades I wanted. Warranty took care of the tranny and I paid for the upgrades. But after all the work performed the F*&ker started going into limp, on The very drive home from the tranny shop, This was very disparaging.
8th--I installed a posi flow pump after getting home to make sure it was not air causing this issue and to put all my doubts to rest on that fuel being the cause.(still limping)
9th--So I at this point I knew it had to be the turbo, took it to the mechanic to see if I could get my warranty to cover this as well. They did, not a new one as my warranty was poop but they did have my Turbo rebuilt by a great shop here locally that has dealt with this exact turbo before. I'm back on the road.