95 LT1 miss at idle, good with gradual accel, bad with a stomp

[butterg]

I know it's not what Caprice lovers want to hear, but I gutted a 95 Caprice (rolled in pursuit, after a complete rebuild only 2kmiles prior) and put it all in my Jag. The computer and harness were done by a reputable place up in Michigan, so I don't think there's any problem there. Got brackets, hoses, exhaust, driveshaft etc, from a reputable place in Texas--so what I'm saying is that it's MOSTLY professionally done.

Here's the problem: It's sometimey.

Constants (Always behaves this way):
smooth idle until warmup
rough but not shaking--just "puffing" noise at tailpipes
Outstanding acceleration given gradual pressure on pedal, hot or cold
Outstanding hard acceleration cold

Sometimey
Sometimes, hard acceleration (hot) from a stop is really bad.
Sometimes, accelerating from speeds over 40, it runs really rough.

I had thought that the sometimey behavior went away with cold weather, but now it seems pretty constant throughout the year. I was suprised at how black the EGR and plugs were when I first acquired the engine 4 years ago--they are not as black as they were, but all plugs are in the same condition; the EGR is new last year, plugs are new 2 years ago, wires new 4 years ago. I put teflon tape around the knock sensors. Couldn't determine which cylinder(s) had the miss when I unplugged injectors one at a time. I took the fuel rail out, presurized it and didn't notice any injector leaks, but could be there. Drove around with a fuel pressure guage taped to the wipers (for a day or two), didn't notice unusual highs or lows, but could be there. Temp is around 100C, regardless of weather.

More to say, but will let you catch up.