Hi LWC,
I don't know of anywhere to download an MX6 manual. I do have a spare MX6 125,250 & 400 Operators Manual. Its a small format owners handbook, but it's pretty comprehensive with sections on timing, carb and suspension tuning, wiring diagrams, brakes, trouble shooting etc. It's in pretty good nick and you can have it for $25 or swap for Can-Am bits etc.
I also have a copy of an original MX6/Qualifier factory Shop Manual which is pretty comprehensive. But I don't have spare, and I don't have the facilities to copy it for you- sorry about that.
Let me know if that's any good to you.
Cheers,
Martin