Final update, got this thing totally sorted out. I got the WGDS working finally, but in the end eliminated it.
First a big thanks to all who posted here to help me get it done. You guys definitely helped me quite a bit.
So now to the solution. First, I found that two of the lines going to the WGDS were crossed by one of the previous owners. Funny thing, the first time I worked on it I found one of the clamps about 1" down the hose which I found odd - so definitely someone had messed with it and plugged the two larger connections in wrong.
On my test drive with the WGDS hooked up correctly I noticed two things - first that boost around 3k rpm didnt come on smooth, you sort of felt it waiver a bit. Second, the boost guage showed a max of 6psi in 1st and second. I recalled from my first drive with the WGDS removed that it was alot smoother, and I got 6.5-7psi on my guage. But I had the pesky CEL when I did that.
To bypass the valve I simply left the wiring harness for it connected and the valve in place. Then I simply capped the line coming from the intake plenum, and directly connected to the turbo outlet to the wastgate actuator. Now I get smooth boost, 6.5-7 psi in all gears, and no wavering. Plus no CEL.
All in all another RX is back from the dead. Next up is getting the seats recovered and a few other odds and ends, but I'm totally pumped to have this thing running good.