So another update, still haven't gotten to the bottom of the solution.
I've replaced the MAP sensor, which cleared out the P0069 code. The only one I have left is the MAF sensor code, which is because I still have the MAF sensor unplugged.
I'm still seeing smoke, and it still seems to be a bit sluggish under acceleration, but the sluggish part might just be me. According to the scanguage, when it is running right, I'm seeing about 18-19 psi of boost under WOT acceleration-I don't know whether that's normal or not. Here's what I've done so far to try and fix the issue.
EHM has been done.
Upgraded filterhead was already installed, however, was still getting air in the lines.
Replaced the rubber fuel lines from the tank with Marine Grade lines. Still getting air.
Installed an inline Airtex pusher pump, and that solved the air in the lines. Plunger is now rock solid.
Replaced the factory CAC hoses with SAMCO hoses.
Verified that the hose from the stock airbox to the turbo was still intact. Hose was solid, no signs of wear or cracking.
Replaced MAP sensor.
Pulled the intake horn off (that was a

) and cleaned it out, was pretty plugged up, and checked that the FCV moved freely. reinstalled the intake horn.
I did cut the cat out of the system, however for now, I'm still running the stock muffler, just because my wife was pissed that it sounded like a dump truck with a straight pipe exhaust. I do need to upgrade the muffler, just haven't had a chance to get around to it yet.
If I was off 1 tooth on the timing belt, would it be noticeable? I would think it would be, but it starts fine (unless hot, but that's another issue), idles smooth, runs fine (except for the smoke and possible loss of power-that could be my imagination though) doesn't knock, and the mileage is still around 26 in town when driven right.
I've verified that the turbo is functioning, by pulling the vacuum hose off, and watching the rod drop, and got about 1/2 in of drop on the the rod. I would think with the MAF unplugged, that the EGR wouldn't be an issue at all, unless somehow it got stuck open-could that cause the issue? I was looking at that, and trying to figure out with the EGR, what I could block off on that, to block the EGR? I don't have the money right now to buy a GDE tune, or a SEGR, but it seems to me that the SEGR has been discontinued? If I were to build a block off plate to go on the output of the EGR, would that work?
I know the principles of how an EGR functions, but not enough to be comfortable blocking off random ports, without knowing a bit more. I was thinking that maybe I could fabricate a plate to go on the two ports coming off the EGR, which if the EGR was stuck open somehow, it would trick it into acting like it was closed-does that make sense?
As far as the hard start, I do have a new CPS sitting in the house, that I intend to install one of these days-just need to find the time to do it. Any help you guys could provide would be greatly appreciated!
Seth