Steve, two thoughts come to mind (I'm trying to put my carb thinking-cap on - it's been awhile other than motorcycles).
Do you happen to know how his idle is if he stops but doesn't use the brakes? If the idle is pretty low (verge of stalling), it simply could be an E- load issue (turning on the headlights or any other big accessory would cause a 100-200 RPM bog that would cause stalling too. It just happens to be the brakes he notices). I hate to say it but for one closed course test (parking lot, no cars, etc) he could disable the stop lights and see if it stalls when he hits the brakes. Just remember to enable the brake lights after the 5 minute test.
One other thought is an issue with the brake booster and a leak. This is pretty unlikely but something to consider if nothing else makes sense.
For now, can he raise the idle adjustment up to compensate for the stalling? I've had to bandaid a few cars this way when they had slightly wrong jetting for cold weather, or the carbs were a little varnished (which can hamper the dashpotting).
I like your idea with the short, but if it was something serious, it should blow the stop-light fuse. Anything less than that should not really hinder alternator/charging system performance enough to cause stalling (the battery acts as a damper and fills the voids).
Sorry to not be much help again but it'll at least bump ya again.
Good luck Steve - it's nice of ya to help him out.