2008 Chevy Cobalt powertrain electrical weirdness

Mid summer, the coolant sensor started to fail to register, but would come
right back when the ECM was reset, every time. Winter came, I let it go for
Spring.
The head, throttle body, EGR, injectors, coils, timing set were all brand-new,
we just did a total rebuild on it last April due to burned-out valves (they were
causing a perpetual misfire condition, it was the only way to eliminate it).

Car ran great, beautifully, all summer, all Fall, all winter, until last week.

Suddenly, it just died. If it didn't have a chain, had a timing belt instead, I'd
have sworn the belt snapped, it was that sudden. Engine code - crankshaft
sensor out of range.

Odd, to me, really, but since we hadn't changed that sensor during the
rebuild I just went and got another one.

BUT

I tried to get it to fire a few times in the meantime. And it would start, but only
if I held the gas to the floor, and the smoke was unreal from the exhaust.

I sat back, engine off, ignition on, literally scratching my head over it. I know,
it said bad crk sensor, but still, something didn't seem right.

Then I noticed a sound under the hood. It sounded like a just about dead
battery trying to engage the starter solenoid, but... The key was just on, not
being cranked, and the battery had nearly full charge.

I got out to see what was going on, pulled off the engine cover, pulled off the
air cleaner housing thing, and lo and behold, the throttle body was flopping
open and closed, and the injectors were firing wildly. And then the secondary
air pump engaged. The whole system started going nuts.

I replaced the crk sensor, replaced the starter relay, and it made no
difference.

Well, I shouldn't say it made no difference at all, since that was when I
noticed I was getting inconsistent codes. crk sensor, cam sensor, MAP, MAF,
ECM not found, multiple misfire, on and on and on, and constantly changing.

So I started opening the covers on the wire harness, looking for shorts.

5v everywhere I looked, where appropriate, 12v also where appropriate, so I
had to go there.

Nothing found in the wiring.

I talked to a few dozen mechanics in my area, and they all agreed - dead
PCM. They said its voltage regulator may be fine, but it sounded like the
programming was screwed.

Okay, so I had a computer custom programmed to my VIN and replaced it.

And it is still doing it.

So I'm at a loss. This thing pumped 1/8 tank of gas into the manifold just
sitting there with the engine off and ignition on. I had to remove it and clean it
out.

I replaced the throttle body, since the TPS and IAC are built into it. No
difference.

It seems to me... Something is shorting the 5v references somewhere, and
it's somewhere that affects both busses (since the crk and cam sensors are
on different reference voltage wires), but wow I'll be damned if I can figure
out where.

Any thoughts?