Engine pulsing like a turn signal!

Riding in 39 miles into work yesterday. Beautiful day bike running like a dream. Last turn before office I get a total loss of power. Glass main blown and flickers and blows back up. Trailer to work and suspect a few things. Put a new battery box in the other day and was thinking maybe terminals hitting seat. Covered with nonconductive rubber. Also found a possible chafe where a terminal on red/wht could have been grounding. Went ape with the biggest can of deoxit I've ever seen (thank you contract company off on Sunday). Taped and generally cleaned stuff up then...... Shit...... Replaced main with a 30a. Everything seemed hunky dory on ride home for about 10 miles at 65 then on off ramp bile felt like someone was turning ignition switch on and off at any rpm above 3800. The higher the rpm the more severe and abrupt the cut off. Rode her home slow. Today, replaced main with a 25 (smallest I have) turn ignition key and neutral light flashing as if it was connected to the turn signals. Also noticed that when ridden and held above 3800, the cutoff was just as rhythmic.
Where to start? I already did the wire clean last month by the way
Recent work was battery box install chain/sprockets and headlight switch clean inspect.
Thanks guys!

Did I mention it's a 77 650 c-1?

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