Does it hold fuel pressure after you shut it off? I rarely see problems with injectors on these even after sitting for years with old gas in them, but one has to wonder if maybe you have sticking injectors. I assume the engine runs smooth, not like it's misfiring or anything like that?
How high is the MAF voltage over spec? I think normally a stock SC will see around 1v at idle but I have not checked that in a long time.
If the 02's are working (you did say they read high all the time) then the most likely cause of a rich condition will be an artificially high MAF signal voltage or injector malfunction.
BAP does not affect AFR, the fuel command comes pretty much directly from MAF signal modified by ECT. It's really pretty much that simple.
The 02's come into play when the EEC tries to close loop, but that takes around 1 minute to 3 minutes or sometimes more depending on a variety of conditions. When the EEC attempts to go closed loop it will first look for a high 02 signal. You indicated that this exists, so then the next thing the EEC will do is begin to remove fuel until the 02's drop and then will begin it's switching routine. So if it's rich on startup, the first reaction you can observe is when the 02 begins to drop. This will be kind of hard to observe because you don't know exactly when it's going to happen. After a fixed amount of time with the trims maxed out (25%), if a lean condition doesn't result during that time, the EEC will "give up" and not attempt to correct again until there is a key cycle. So what I'm getting at is if in your observations you do not detect this happening, you may miss the event entirely and it may never (to your knowledge) even appear try to go into closed loop.
I did notice that you said it seemed lean at WOT, which is puzzling. How did you determine this? Did 02 sensor voltage drop under boost? I know you said you checked fuel pressure, but I wonder if you could have a fuel deliver problem. Does pressure drop under boost? It should rise # for # under boost. So basically 48-52psi depending on rpm (at WOT). It would be pretty typical for you to have a bad fuel pump after sitting, etc., but that doesn't explain your rich idle condition. It may be you have two separate problems going.
Oh, did you say whether you ever verified TPS voltage and sensor output? It's a quick check with the BO box and will eliminate that as a contributing issue.