Yes there is a difference, its small but the S13 has one extra rib on the one of the pulleys(don't remember which pulley has the extra rib). S13 pulley set will physically fit on the s14 sr20 motors. If you are using S14 belts with the S13 pulleys on a s14 sr20 motor, one of the belts will be a tad too thin. You can make it work by swapping the crank pulley and using the correct belt or just ignore the small gap.
The note/disclaimer here just confirmed what I was saying.
http://www.frsport.com/Megan-Racing-...ed_p_1377.html