I'm looking at the Cool Rails, Lil '59, & Vintage Rails. Looking for a warm, rolled off PAFy sound, that matches in output well with the Custom Custom.
I'm running a Cool Rails & Custom Custom with a 500K volume pot in my Charvel Model 4 partscaster:
I love the Cool Rails, but it's brighter and more clear than a PAF; more of a Jazz than a '59. If you're worried that the Cool Rails is too bright, it might be worth looking into the Hot Rails neck.
I don't have any currently, but I used to own an ESP Vintage Plus S loaded with Vintage Rails. They're very close to SSL-1s in terms of output, so I'd be concerned that they'd be overpowered by a Custom Custom. I thought they sounded like a passive EMG-SA, in that they're vintage Strat inspired but more hifi. They're also a bit more compressed and have the balance and lack of dropouts typical of rail pickups.
I'm not super familiar with the Little '59, so I'll let others weigh in on that one.