Re: custom or desortion or c5 for strat?
All will be fairly fat, but the custom and distortion more so than the c5 due to their ceramic magnets. Id say the c5 has a more vintage type tone than the others and might even cut a bit better, but the the custom has more of a fat thick tone and the distortion just takes that a step further...in my opinion of course
If you're after something to put in this strat that is fat but still cuts, i wouldn't dream of going past a JB! Its the best pickup ive ever heard and it does well in so many different styles its just a fantastic pickup. And it would definitely go well with a couple of cool rails, although unless you're totally stuck on putting two cool rails in the neck and middle id put something different in the middle.
The neck is a great place for a hot pickup like the cool rails or a JBJr. or whatever, but in a strat H-S-S configuration you can get so much versatility just by putting something a little cooler in the middle. Something like an ssl-5 custom staggered for strat (or the flat version, whichever really) would be great with two hot pickup in the bridge and neck. Or even something like a duckbucker or vintage rails. Something cooler will give you great cleans when used by itself and in conjunction with the hotter bridge and neck pickups which you can get all your hot sounds out of anyway. You can also then get some really cool sounding single-coil esque bluesy or funky tones out of the guitar if you want them, which you will no doubt somewhere along the line.
I have an alder guitar with a H-S-S pickup config and i have a full sized JB in the bridge, a JBJr. in the neck, and a currently but soon to be upgraded stock single coil in the middle. Now the stock single in the middle isnt that good on its own because its just a crappy stock pickup, but even with its crappiness i use it in positions 2 and 4 and the cleans sound terrific! And i get all the greatest heavier crunchier sounds out of the hotter picukps, not to mention the beautiful jazzy cleans out of the JBJr. neck pickup...but thats another kettle of fish

I soon plan to replace my middle pickup with a custom staggered or flat for strat, because its a little fatter and hotter than a classic strat pickup, while still soundin like one.
So id suggest a JB for the bridge and a custom staggered or flat in the middle instead of another cool rails. That combination would be killer. Also if you want one of the pickups you mentioned above another killer combo would be the custom in the bridge with the custom staggered/flat middle and cool rails neck.
But my first choice would definitely be a JB in the bridge with the above mentioned middle and neck.