Okay fwiw the description of how it runs reminds me of what used to happen back in the days of distributors. If ya missed a coupla teeth on the way back in the motor usually ran as you describe. Or...a more ominious thought just crossed my mind, skipped teeth on the timing gear set, but I don't think that applies to an LT5, I hope.
Disclaimer: I'm okay with a 70's sbc, I'm not fluent in LT5 yet.
My first impression was exactly what XfireZ51, miss placed plug wires. I can go look up the firing order in my Helm if need be? See I told ya I'm not fluent in LT5, heck I don't even remember the firing order on my 72 LT-1 that I had a long time ago (I'm also getting senile!).
I would wonder if a scan tool would diagnoise a problem with the DIS box? That's the only other thing I can think of, unless there is a insulation problem with the harness that connects the coil plate to the DIS box? Can the plate go bad?
I shouldn't even post this as I'm lost on diagnoising your issue.
Tom
I know you don't want to hear this Greg, but simplest things first. Firing order, bridged plugs, wires okay, coils seated properly, DIS wiring I believe is "Keyed" so you really can't put individual harnesses in the wrong spots or 180* off (I'm fairly sure on that point). I know there used to be a lot of defect issues with aftermarket coils a long time ago the experienced guys said to stay with GM coils. That's all I can think of right now. Sorry for my lack of help.