I have a stock shifter from my '04 Raptor 660 that sounds like it is the same setup. Does yours attach to the inside of the foot peg?
I thought that setup was sloppy so I bought a Pro Design billet 1 pc that comes directly off the shift shaft (no linkage and ball joint) now it shifts a lot better. I would recommend replacing it with a 1pc. They are about 60 - 80 bucks. Got mine off E-bay, but a lot of the parts places in Dirt Wheels have them. Try ALBA or Rocky Mountain ATV supply. I would give you my stock one for free if it is the same part for 350 and 660. You would have to pick it up or pay for shipping. I have a feeling that with the different engine, the shifter length or angle would be different.
if u could ship the stock one to me i will pay for the shipping it might just work, if not a friend of mine dad is a handy man a will torch it to make it fit , i will have to look into it...