Update:
Have never quite resolved all the "weirdness" of my charging system. The alt will at times shut off (flashing amber indicating low voltage), and at times it will go into what the Niehoff troubleshooting refers to as "OVCO" or Over Voltage Cut Off (flashing red on the 28v LED).
After quite a bit of testing, cleaning and replacing connections, going over and over the troubleshooting guides, and talking to some experts at Niehoff and one of their largest repair facilities I believe I have found the issue.
Upon testing the alternator output for AC ripple, I found the rectifier in the alternator seems to have issues and is allowing a LOT of AC to get through. Usual acceptable levels are about +/- 0.20v. I'm seeing +2v and up to -5v spikes in the scope trace (AC coupled). I believe at times this is confusing the regulator. Especially during periods of rapid engine acceleration or deceleration - I can often cause an OVCO with the fast idle switch which causes a fast but very slightly surging idle.
Unfortunately the "rectifier" portion of the alternator is the entire drive end bell assembly (rectifier is potted into it) and the cost is about $1200 - coupled with other rebuild parts and labor it would put the cost to repair the unit too close to the cost of a replacement given that rotor, stators (4 of them) and regulator would be reused - a new unit would contain all new parts for not that much more.
So I'm not sure what I want to do at this point. Suggestions?