Okay, I did some inspecting and measuring and I got no friggin' clue.
What I did was, I said berk it all. Revert the whole dang setup to the last known system. I dug out my previous MS box (a freebie handbuilt MS1/3.0 unit that had issues due to less than good assembly), found my previous set of injectors (GSL-SE 680cc), for good measure I connected rotor 1 to Inj1 and rotor 2 to Inj2 instead of ganging them on one driver. Just because.
At this point, I noted that the injectors could rotate freely in the rail when the rail was bolted down.
Pulled the spark plugs, blew all the fuel out of the chambers, put that back together, booted TunderStudio, and, yep, it's reading 187F air temp, which is non optimal. When trying to start, the engine kicked but stalled out right away like insufficient fuel. Well, what the hell, I'll just take the req*fuel and bump it up 20%.
Started and ran, all by itself. It never sounded so good as when it ran normally without chemical coaxing
So I went backwards from there and connected rotor 2 to Inj1, ganging them like I'd been doing since I first installed Megasquirt when I swapped a stock GSL-SE engine in one winter. Starts and runs good. Okay, now the moment of truth... Unplug the MS1 box and plug in my MS2/Extra 3.57 box.
Starts and runs just fine, even without retuning!
It was the injectors all along. The injectors that sprayed beautifully when the rail was pulled out of the engine and I was using test mode, leading me to think that they couldn't be the problem and move on to other things.
Here's what I think happened. I noticed, but didn't think much of it, that the RC injectors could not rotate when the rail was bolted down. It only struck me as odd after the fact when I noted that the GSL-SE injectors could spin freely. Shortly before the engine started running on what sounded like one rotor, while trying to limp the engine home with only leading ignition, it hiccuped through the intake a time or two or five. I think the intake backfires damaged the injector bodies, expanding them or something, so that they were now getting crushed by the fuel rail. They sprayed beautifully when the rail wasn't bolted down because they were no longer being crushed. But in the engine they were unable to open properly.
The really odd thing, which makes me think that I got counterfeit injectors somehow, is that the engine runs just fine on injectors that are theoretically only 68% the capacity. I noted that my peak power duty cycles never really dropped after switching to the 1000s, but I also changed from the MS1/3.0 to MS2/3.57 (maybe a calculation difference?) and removed the boosters from my carb's venturis (maybe more airflow?) so I just sorta shrugged. But now I wonder.
One thing I did learn through all this is that the GSL-SE base fuel pressure is, in fact, 2.5 bar. I never knew. But now I know, if I want more flow, I should just get an FC primary rail (no regulator) and use an adjustable regulator. Or just convert the car to returnless with a $20 Corvette fuel filter that has a built in 58psi regulator... sounds like a better idea IMO.