His fuse is taking 40 seconds to blow, that implies a slight overcurrent, say 50-55 amps. You have TWO 40 amp fuses downstream to the brake controller - 40+40=80. So, something out of whack with the brake controller could cause a total current of well over 40 amps to the brake controller and yet NOT blow either 40 amp fuse.

WHile it could be something in the pulse module, I'd yank each 40 amp fuse out and put an ammeter in there and see what currents I have thru those two fuses. If I saw little current, then I'd try to verify the diagram (our wiring diagrams are not exactly 100% accurate) to be sure it HAS to be the pulse module.

Here is something to try: Start the car and YANK BOTH 40amp fuses and see what you get. If the 50amp won't blow, you KNOW your overcurrent is downstream of the 40amp fuses.

YOu've got to chase this like any other DC current issue.