The booster gets its vacuum from the throttle plate at the back of the carb. It IS unported manifold vacuum tho. The trans is getting vacuum from a port on the back of the manifold.
The brakes are not very well assisted as it is so unplugging it wouldnt hurt much. I'm pretty sure that its got to be related to that tho, or else its just coincidence that the engine stumbles and dies when i apply the brakes - even when sitting still.
Could the trans modulator go bad from getting wet? I power washed the trans with hot water to clean it up some before i installed it, im sure the modulator got pretty wet but I didn't get any water in the trans itself.