When I ordered both of my Jakes back in the day, I specified Hipshot Ultralite tuners and a Hipshot bridge, both of which are very nice, but obviously bumped the price up a bit.
Having played a few 'stock' Jakes since, I think I could probably live with the standard BBoT bridge, but not so much the tuners. They just don't look substantial enough to me, but I accept it's more than likely psychological.
As for the pickups, my original had Haussels which were great - quite warm. My LPB has stock Maruszczyk's, which are just the bee's knees. Love them.