What carbs, needle jets and main jets are you running at the moment?
With my first RD400, I ran pods and stock pipes and every time I rebuilt the motor after yet another meltdown, I went up another bunch of main jet sizes. I eventually changed the needle jets and that fixed it, but I was spending more on pistons than fuel for a while.
Do you have access to a dyno locally that you could strap it down and see what the air:fuel mix was doing?
Did you clean the carbs ultrasonically or just the obvious corrosion? I went back through the thread quickly and those carbs were pretty bad and it makes me wonder if there's still some crap in there.
Can you borrow a pair of RD400 carbs from someone that we know work, just to see if swapping them cures the problem.
You might also check the coils and that Newtronics - use a car type timing light and see if it still lights up on both sides as you rev it - or does it miss sometimes. If it's not a steady light, borrow some coils. I have sets of 3 ohm dyna coils on the shelf if you need a set.
Another thing to check is battery voltage. If it's dropping as revs rise, that could be the issue.
If you were closer, I'd suggest you bring it over, but that's not so simple from TN to northern IL.