First a big thanks to Aaron for helping me with this. And Andrew was a great help as well (ps he did wind up calling me on the way home).
Quick background for whoever wants it. My Hydra was installed and ran great for about an hour. I shut it off for a few minutes and then started to drive home. In less than a half mile my throttle response completely disappeared and my idle ran up to about 2200rpms and wouldn't drop. I couldn't find any problems with a vaccum leak or a kinked hose or anything. Went back to the stock ECU and everything was completely fine. Spoke with Phil and Andrew and shipped it back to Andrew to have the firmware flashed and the harness upgraded with a relay. I got the Hydra back and put it in last night. Everything was fine last night. Everything was fine on the way to work and on the way to Aaron's house after work. Aaron helped copilot and work on the PWM4 map to try and help with some overboost I was having. I did at least four good pulls and had no problems. Pulled in to park for a bit, shut off the car, restarted it, then the idle ran slowly up to about 2200rpms and held. I still had throttle response this time though at least. I found that if I barely applied pressure to the throttle, sometimes tapping it barely, I could get the throttle to settle back down. If I revved it hard, it would climb back to 2200rpms and hold. After some time spent on the phone with Andrew we tweaked the PWM2 map and things seemed to be better. But the car hadn't been driven hard since it cooled down while working with Andrew.
So on with the rest of the story. I stopped half way home and shut off the car for five minutes. When I restarted it, the idle was a little high for me, maybe 1100rpm when normally it idles at a nice low 900rpms. I goosed the throttle and it started its slow climb up to 2000rpm again. However I had a real easy time with the slight tapping trick and only took a second to get it to settle back down.
Then when I got home I shut it off for a few seconds and then restarted it. Same thing again. It seems like it still wants to climb, but it is way easier to get it to settle down. And what else is really weird to me is that if I pull up to a light and throw it in neutral the idle sits real steady around 900rpms. It is only after I shut it off and then restart it. But at least now it seems to be a little more under control.
Of course I am also curious if the fact that it was cooling off through the evening had any impact on the problem. I am hoping that the changes made to PWM2 really have helped and not just the ambient temp difference. I guess I will find out tomorrow. Definitely keeping my stock ECU handy for that trip to Norwalk.
Thanks again Aaron and Andrew!!