I am sure you could get a custom wheelset for your money that is lighter, stiffer (maybe) and more aero than a Ksyrium sl wheelset but I'm not sure it would have the same bullet proof quality. Ksyiums or say Campagnolo Shamals are system wheels and will spin and spin forever. All the constituent parts are perfectly matched. The other problem in my view with custom is warranty. Buy your Mavic or Campy wheels from a good local retailer or good online company and you won't have any warranty problems. If there are parts problems with handbuilt the builder will most likely have to send back constituent parts back to his surpplier with resultant delays.
uhm, ever had to replace a broken Ksyrium spoke?Good luck. Thats if the nipples havent corroded into the rim making replacement impossible. Mavic hubs arent the best either...
You can easily build a wheel thats lighter, cheaper, more servicable and with replacement parts significantly cheaper and more widely available these days than a Ksyrium SL.
Oh, and Mavic Ksyrium SL's are less aero than a pair of bog standard 32spoke low profile wheels(Proved in numerous tests) Those thick Zicral spokes are about as aerodynamic as a brick.