Welp, some good and more bad news. Got the axle back in and loctited the bolts in for insurance. Took it out for a drive and it did fine, but noticed that the vacuum pump had almost come out! I pushed it back into the hole and loctited it's retainer bolt as well.
Fast forward a week and I tried to install a manual boost controller made with a combination of a pressure regulator and pressure relief valve in line as per here:
http://www.autospeed.com/cms/article.html?&A=111348 . Wow, did NOT like that! First test drive was just a small turn in on the regulator, but the first time I tried a 2nd gear pull, there was a loud BUMP/POP followed by grey smoke and the engine nearly dying, sounding like it was only running on a couple cylinders and bogging down when I tried to give it any pedal. After about 20-30 seconds it returned to normal idle and acceleration operation and I soft-shoed it home. There is no coolant loss, and nothing is leaking around the head mating are that I can see right now. It's a repeatable fault, as I have demonstrated earlier this afternoon. What's more, I looked under the hood and saw the vacuum pump doing a little twirly jig in it's hole! I'm going to have to pull it back out and see if there's any oil pump shaft, intermediate shaft, and/or vacuum pump damage. As far as the power loss incident, I am actually at a loss of what it definitely might be. I'm obviously thinking it's something to do with the boost controller I made, either causing a few things to happen:
-The LDA is seeing too much signal boost and the pump dumps too much fuel
-The timing is too advanced and a cylinder pre-ignited
That is really all I have right now. I'm going to be removing the controller and go back to just the wastegate for now. I don't like these valves, and will most likely go for a more proven boost control setup down the road rather than this hodgepodge air tool junk. I will also need to check out the vacuum pump situation, as well as get an eye in the turbo compressor as well as around the exhaust area; she wasn't as willing to spool after the first incident. I can only hope my stupidity and impatience hasn't caused major, expensive damage yet.