Found the no start problem, it was the vacuum "manifold" that plugs into the intake that has the brake booster vacuum line hooked up to it. The port on top broke inside the vacuum hose that now leads to the waste gate and the vacuum manifold piece pulled out of the intake. Got another one on and starts and runs.
I don't know if this is related or not but I am now seeing some random misses on cylinder 5. Seems to run fine though, and since I've driven it the misses seem few and far between from what I can feel, but now since I've tried some hard accel where boost is achieved the car seems to stutter and stumble, almost feel restricted, and the turbo under medium throttle sounds weak, under hard throttle sounds strong but definitely bucks. Don't want to hurt the engine so I'm going to try to get a scanner on it and see what I can see driving around.
The only thing I tried when I saw the miss upon start up of fixing the problem was a new spark plug wire, used known good coil, swapped plugs. I had cleaned the MAF prior to finding the main problem of my no start, don't know if that caused anything. I did not touch the MAF sensor wires, but the MAF sensor (LT1) is 7 years old (from when the kit was put on the inital turbo 04 GT).
I had swapped ICM's before I found the disconnected vacuum manifold, but have since swapped the original one back on before I got it running.