Dude the 59/Custom hybrid is such a great pickup. Why on Earth would you want to replace it? Well, I get it so anyway... Look, believe it or not, the AT-1 makes an excellent pickup for mahogany and alder guitars. It has a bit too much sizzle with ash. Based on the pickups you mentioned and wanting to get away from the usual, these are what I'd recommend:
Bareknuckle Riff-Raff/Mule set - Loud, but output is less than an AT-1
Bareknuckle VHII set
Bareknuckle Black Dog set
All of these pickups are rather unique in my opinion and are a departure from your circle of pickups, but not too far off or too high in output. Now, I'm going to give you a suggestion, but I've been really impressed with this pickup, so hear me out. Try a Dimarzio Transition. In mv output according to Dimarzio, the AT-1 is rated at 320 and the Transition is rated at 390. Even so, it's really not as hot as you might think. Lowering it a bit from the strings will give you the perfect output. At first, it seems like a pretty straightforward pickup, but it will sing for you like a canary. It will respond to your pick attack like you're in total command of a battleship. It has clarity and definition, but it's warm and will give you whatever you want with the turn of a dial. It cleans up fairly well, so if you have a Marshall and want clean tones, it will be only a little hotter than an AT-1 in terms of how much it will push your amp into overdrive. If I'm wrong, you can always exchange it.
Lastly, I suggest putting your 59/Custom hybrid in the neck position and putting a Duncan Custom in the bridge. You'll freak out on how good of a neck pickup the 59/Custom hybrid will make. Overall, it will be on the hot side, but the tone will be so damned good dude.