Update: I'm driving in a loaner 2011 Impreza for now.
Here's the actual update: I continued to have the same issue even after 3 times bringing the car in and having the learning reset. I can reset the learning from my AP even without it married to the car (which I found out recently!). Friday I took it in (as a 3rd trip) and the tech rode with me and I was trying to cause it to run at the lower boost and misfire. I couldn't, and I felt like an ass with the tech in the car as I drove the car with a few WOT pulls and couldn't recreate the condition to cause it to reduce boost. I brought it home, tail between my legs, and was happy that the car was at least running okay. I kept it stock, as I prefer stock speed to less than stock with aftermarket parts. I married the AP to the car so I could monitor things, and within 5 minutes of flashing to stage 1 the car acted like a dog again. I flashed back to stock married mode and it ran okay for a little while, but as the learning continued it got worse and worse.
I unmarried the AP altogether to eliminate that as a possible variable, and ran through an entire learning cycle. This morning I took it in with it acting funny again, and the dealer knows me by name (I'm not ACTUALLY proud of that), and the tech hopped in and I successfully was able to show him what's happening. He replaced the boost control solenoid, and then said he wanted me to drive it to see if I thought it was fixed. I've figured out it's when I'm driving normally, and shifting at approx 3K like I regularly do that the car acts the worst. I got on the freeway with the new BCS in with the tech in the car too, and it was still misfiring between 2500-3000 rpm. To be clearer, it misfires at that range, and then the boost gets pulled after a little while of misfiring and it will no longer boost fully above 3K either. I know it shouldn't really boost at 2500.
They gave me a rental as they're not sure what it's going to take to fix it now, but at least we figured out how to make the car fail. . . That sounds wrong. I mean I can recreate the malfunction. I'm SUPER impressed with the service I've been receiving, especially after the last visit I had where nothing could be recreated. As long as it's getting fixed that's all I care about. The car is completely stock now so they're happy to continue diagnosing it. It wasn't a bad tank of gas, apparently. I am kind of excited that it's actually getting fixed. I almost started to get used to driving around at 8-9 PSI. I found myself second guessing that maybe the car was running okay. I can't imagine how much faster it used to be any more.
I know it's not fixed yet, but being that they gave me a car to use while they work on it, I don't really care how long it takes. I have to give props to Mark Miller Subaru for great service thus far, and I will absolutely continue to shop there, and Geoff (the service rep) and Josh (the tech) have just been awesome. I'm so satisfied just that it's not just me thinking my car is running like crap. We'll see how it goes from here on out. I'll update it when I get the car back.