You said that you are using a sx ignition on your 1000 did you have to modified the case were the trigger coil mounts. I have a 00 which used a smaller flywheel diameter and I am trying to put a 98-99 stator and flywheel in but the case and trigger coil are to close and will not let the flywheel go on. I tried using the 00 flywheel but I don't get any spark. The flywheel is different and does'nt seem to go far enough over the stator. I really hate to buy high rpm cdi as I have already purchase a wiring sx wiring harness,cdi and the stator and flywheel is the same as the sx. I thought about a msd ignition but then I would'nt be able to run Imp. stock. Any help would be appreciated. 
Srxspec
Your #1 performance shop!
Danger, you will have to modify the cases. I used 98-99 cases which allowed me to not have to modify anything.
Thanks, that is what I thought but hoping not. I looked at msd web site and they don't list a ignition for yamaha, but there is a picture of a vmax 4. Thought that was funny.
Srxspec
Your #1 performance shop!
In order to run an MSD ignition you will have to make your own Ignition Plate as MSD doesn't have one. The reason for the Vmax-4 being on there is because it uses a different ignition which MSD does supply, unfortunately it won't work with a 3 cylinder.
Well I got it to work. Ground the case .040 and redrilled and tapped new holes for the trigger coil to make room for the flywheel. Now I have spark. But still no pipes. So much for racing it this year. Should give me plenty of time to get it dialed in for next year. I may try it on the grass this fall. Mark at Price would like to see me run it on the tar but I don't know if I can find the funds to set it up for the tar, spent quite a chunk of money already and have'nt even ran it yet.