switching from 2 phase charging to 3

i have a kz550 a1 and recently ordered an stator and got the 3 phase 18 pole stator instead of the 2 phase 12 pole stator so i decided to order the regulator rectifier for the 3 phase and change it over the bike runs now but drains the battery i am wondering if the rotor is diffrent to and if im also going to have to order that to correct the problem

I doubt it's the rotor, thats just a wheel with magnet(s) on it. If it is not charging, the regulator/rectifier assembly is probably not hooked up right.