Thanks for the response. That helps me narrow things down some.
The o2 sensors are factory original I'm pretty sure, with 84k miles. 10k of which was boosted miles. The PO was a road course guy and from my guess it's got over 15 hours of open track time, so I'm sure the sensors could stand to be replaced even though they are switching as they should on datalogs. I do know they can get lazy over time. I pulled both front o2 sensors to swap them from side to side and noticed bank 1 (the rich side) was darker than the other. Imagine that. Switching them had no effect on STFTs.
I'm also aware <11.0 AFR is getting into pig rich territory, so the base tune could very well have killed the sensors.
As for fuel pressure, I can make the delta pressure spike to 55-70psi by slamming the throttle closed, and I assume that to be a good sign. At cruise it hangs out at 37-43psi.
I have not touched the intake manifold but with the age and mileage of the car I guess I shouldn't rule it out. I'm going to start with looking at the items I've touched. So replacing injector o-rings and o2 sensors will be the first things to be done. Though I would think if I had a bad o-ring there would be a fuel leak..? I will be running Seafoam through a vacuum line to see if any smoke seeps from the engine. Spraying carb cleaner on random vacuum hoses got me nowhere.
I too, have a messed up COP clip. I've secured it with a zip tie and moved on thinking it's fine as long as it doesn't slide on and off by itself. Spark plugs have 10k miles so I guess those can be replaced too. Plug boots have recently been replaced for maintenance.
If you swapped sensors from bank to opposing bank and get the same readings, your O2's are good. While replacing them could be considered preventative maintenance, if you want to save the cash then keep flying what you've got.
As for the manifold gaskets, if they haven't been messed with, odds are they are fine. The gasket rings are actually stout pieces, unless they get dried out and/or pinched, they will usually out-live the motor. It's worth a look if you have the manifold off, other than that it sounds like they haven't been molested.
Seafoam is a great smoke show out of the tailpipes but won't get you anywhere under the hood. If you're going to do a smoke test on the motor, get a specialized kit for it. You'll also need an air compressor with a pressure regulator set low enough not to damage components or pop lines off. Smoke tests, IMO, will only really show major vacuum leaks. If you had a major leak, you'd know it. AFR would be lean, engine usually runs crappier, and spraying carb cleaner would definitely have an effect. I only mentioned my vacuum leak because it was cylinder specific and hidden. Took me forever to find, and I only found it by happy chance. Had I sprayed carb cleaner around the intake runners at the head, I would have found it faster. But I didn't think the gaskets were compromised.
Spark plugs may not be a bad item to at least inspect, although replacing them at 10k/mi is a bit of a waste, unless they are fouled beyond cleaning up. If they are bad at 10k there's other issues at play (usually tune related) but would certainly depend on the method of fouling (over-fueling or having oil on them). Making sure their gaps are very consistent is important. If you have half of them at .035 and the other half at .040 it theoretically could affect fuel trim readings as the combustion events may not get even burns (such as cylinders on one bank aren't burning the fuel as completely as the other bank, which again the stars may need to align for), but enough to throw it off .10-.15 from bank to bank, it'd be a longshot. I may be talking out of my ass on that, as from my understanding the only reason a FI user needs to shorten the plug gap is to suppress spark blowout under boost. Most of my reading on plugs pertained to fuel efficiency, but on that process I relate it to performance as one effects the other. Still, a visual of the plugs is always good to see when having engine issues pertaining to fueling.
I've not seen many injector related issues, although having a bench flow test done on them never hurts. I would make sure a reputable shop who knows what they're doing does this. Having a local jiffy lube or the like "blow out" your injectors isn't going to do much. The injectors have screens inside of them to prevent micron sized debris from fouling the tips. If a tip were fouled, it would likely cause a bad spray pattern, or partially clog the injector. Blowing them out wouldn't fix this, only rebuilding the injector would. There are plenty of youtube videos on how to DIY injector cleaning and rebuilds. But only a shop with a bench flow can tell you if your injectors are performing properly.
The last thing I can think of has to do with the fuel hat. I'm not as familiar with the GT500 pump setup as I am with a stock or modified GT hat. So this is pure theory. However, on the stock GT hat, there's a "T" in the supply line. From what I can see of it, I'm presuming that the opposite end of that line goes to the saddle pump that pumps fuel from the P/S to the D/S of the tank. In essence, it's pretty much just standing pressure. The other side obviously is the supply end of the primary fuel hat, and the long run of the "T" of course feeds the engine. In order to swap hats, this "T" has to be disconnected to remove the hat. Is it possible when the GT500 hat was installed, the "T" was not clipped in fully, or perhaps the O-ring in the connection was damaged? I find it odd that the GT500 setup is spanked at 100% duty cycle on your setup. The margin of safety for most tuners is 85%. Some may allow for higher as long as fuel pressure and AFR are in tolerance and it's at the end of the run. It's too bad you don't have a 30A BAP available to hook up, would be a good test on duty cycle, to see if there's a difference or if the pump was actually run out. My idea is that once the pump is really moving, it's actually leaking in the tank at that fitting. I don't believe this would cause fuel trim issues, but it would spank your pumps.