ah, ok I had missed that in the book (pulled up the PDF). you got a lot nicer brake than I did
I put the Pro Series POD in mine last week. which took the same harness as yours (cequent automotive makes pretty much all the brake controllers except for hayes. they all take the same oem adapter harness).
if it's not super loud I wouldn't worry about it, or your hearing is super sensitive to these types of noises, more so than mine. sounds like it's either the stop switch on the pedal or one of the relays. there's over a dozen relays & fuzes for the towing alone on the truck. that 7 pin connector does quite a bit: all the trailer lights (signal & marker), 12v power to charge batteries, and the electric brakes.