Does the idle speed also vary?
I've owned a 383 that sounds like your combo except an AVS off a 440, and while the idle was choppy, I wouldn't say it ran roughly. In fact it pulled really hard above approx 3,000 RPM. But because it had a fairly tight converter, low-RPM response was rather soggy.
"Rough" - depending on how rough, how consistent, and when - might even be in the valvetrain, but 1st I'd want to try a different timing light and double check the harmonic balancer to see if it's failing. Are you sure - if by rough you mean the thing's shaking - there isn't an external balancer or flex-plate/flywheel on it?