Hi there

I picked my '94 900RR up a few weeks ago and I have been riding it around. Last week I went to pick up a CBR600 Hurricane and left my RR out side and we got heavy rain
So the next day I went to take the RR for a ride and noticed that if I Was at low RPM and got on it, it would spudder and choke but if I held it up like 3000RPM it was fine so I figured this was the carbs so I brought it to a shop and had the carbs cleaned.
Dropped it off Saturday, had it back Wednesday.
I've been riding it for the past few days but last night I went for a reasonably long ride with a friend, about 45 minutes in it started doing the same thing so I thought it was a carb issue. But I went to beep my horn and it didn't beep and I noticed my lights were dimming.
If I held the horn button and tried to accelerate, it would spudder and die even worse. We got off the highway and it finally died.

I'm wondering if I cooked the regulator or something worse. My old 1994 CBR600 had a bad voltage regulator and I was able to upgrade it a using a later GSXR750 regulator.

Unplugged the regulator with a good car battery attached and the bike runs a million times better.
Purchased a GSXR regulator just like I did for my old CBR F2.

Installed GSXR regulator, same issue. Bike does not charge. ~35V at each of the yellow field wires under the seat to the stator @ 5,000RPM and between each yellow wire I Have .4ohms of resistance
Unplug regulator, bike seems to run better. All wiring gets hot still

Sorry for the long winded post but thanks for reading.
-Garrett