Flickering Lights

Well I don't know. You still have a bulkhead connector, or is it eliminated?

make some voltage tests. You will probably have to make up some stuff so you can access various points.

Get the thing fired up and running, and flicker "the worst" you know how to make it

Check voltage direct from battery NEG post to the regulator mounting flange. This "should" be close to zero or zero. Even a few tenths of one volt is a poor ground path

Check voltage between battery positive post and the VR "IGN" connection, that is switched 12V. Once again, this should be close to zero. More than say, .3V (3/10 of one volt) means look into the circuit path from battery, through the harness and ignition switch to the VR.

Check the path from the VR to the field. Once again, bulkhead? connector?

How big are the grounds battery to body and to engine?

If nothing turns up there try a different regulator, and if that doesn't fix it, try a different alternator, regardless of what is claimed "it is good."

Is the Francis setup connector pre-wired? I believe they use a Ford based or GM based regulator, set up to eliminate the idiot lamp. That is, could the connector be wired wrong?