Here's the latest info in my smog parade:
I took it to a shop here that was listed with the California Bureau of Automotive Repair (BAR) as a Gold Shield Guaranteed Repair (GSGR) shop that was also certified to smog and pass Gross Polluters (GP), which unfortunately with my most recent smog check my car has become.

I found this shop using the
www.smogcheck.ca.gov website (for other CA-based SHO owners).
So, I get to the shop, and the mechanic has me bring the car around back, since all the bays were full. I popped the hood for him and he just stands there looking around at the engine without really getting into it. He basically says "this engine isn't normal"
I describe how I've had my O2 sensors and cats replaced recently, had a 60k service done within 30k miles, had the fuel filter replaced within the last 10k miles.
He seems a little baffled, but still confident that he can do some diagnosis. I can tell this guy is really experienced with troubleshooting engines, so I'm listening intently to his every word. First thing he does is disassemble my 80mm MAF and check the connections. They are all clean. He puts that back together. I guess at this point I should have realized he was looking for reasons for me to be running lean.
After this he pulls back the tape around the TPS wiring, and hooks up a voltmeter to it and the battery. He tries several locations for the ground connection, and finally settles on the battery itself. He has me place the key in the accessory position, and starts taking readings off the green TPS wire while moving the throttle by hand. Eventually he explains "see, the black wire is ground, and the red is +5V from the ECS. The green wire varies up to +5V depending on the location of the throttle. At WOT it should be sending +5V, but yours is only registering +0.1V. To me it seems you need to check the green wire all the way back to the ECS, or the ECS itself may be a problem. Have you ever done any programming with the ECS?"
I say I have, because the SHO Shop put in a custom LPM for my intake and exhaust upgrades.
He says the ECS might be bad, shows it to me where it's mounted against the firewall and says to take it out I'd have to remove the dash. He then says "take it to a Ford dealer, they can hook up an inline computer and have it diagnosed within one hour. I don't have the necessary equipment, but I can do a full diagnostic over a period of a few days. But take it to a Ford dealer. Otherwise you are just wasting your time."
So, to me this kinda all makes sense. If I am really running a lean mixture because of faulty TPS readings, then that should raise my combustion temperature and thus causing excess NOx emissions as noted above.
Anyone have any comments, ideas, or similar experience? Has anyone's ECSs ever failed on them like this?
I feel much more confident in knowing that I may be able to fix my engine after having this mechanic look at it.
Thanks all for tagging along on this super-long message!