IIRC, on gix, they don't use tire speed to calculate mph. not entirely sure but i believe the speedo sensor is hooked up somewhere near the driveshaft. best to ask the gixxer.com board on that. i don't think any bikes have the speed sensor on the tires/rims. i put the bike in gear on the rear stand and it did read a diff. mph on both the gix and R6. the R6 didn't have a chain at 1 point cause I was doing the 520 conversion.
the best way to correct it is to use the yellowbox speed calibrator. there isn't a way you can mod your speedo to adjust for sprocket changes. it's either the yellowbox or switch back to stock gearing.