If your current cables to do work on the new bars then you will neet to special order cables .  I use Barnett for my source of cables.  You will need to mount the new bars and then measure the new length for each cable or brake line to within 1/2" of possible.  Use a piece of used electrical wire, like from an old lamp or toaster, that wire is flexable enough to bend the they way you want it to go, and lay it along the exact route you want the real cable to follow.  Start the beggining end at the bar lever control and route it to the carb, or clutch attachment, or to the brake caliper and mark  the place on the wire the place for the new attachment.  THEN pull the wire off the bike and lay it on a flat surface and measure the exact length needed.  
Whoever you choose to make the cable need to know the exact length of each one, and also for the throttle cable they need to know the type of attachment for the hand throttle on the bars (there are 3 types depending on which model year Savage/S40 you have) and and the type carb to be used because there is a lot of variation in all the motorycles out there.
I have all the specific info needed to make cables for any model year Savage or S40 and for the stock carb or Mikuni VM or Amal or Edelbrock Quicksilver.  It makes for alot of combinations.  I spent over 6 months with their tech section to get all of the combo's correct.

If you choose a different cable source then be prepared to send some of your cables to them so they will be able to make an exact match.  It just depends on if they have done LS650 cables in the past and already know what they look like.

A full set of throttle, clutch and brake line can total in the $150-250 range, depending on the type of sheath you choose.  Black vinyl is the least expensive

These are what Barnett offers...

BLACK VINYL


STAINLESS


PLATINUM


STEALTH SERIES



I hope this is helpful.  If you need specific advice on some aspect then just drop me PM.