If you're on a two-stroke, your cases fill with fuel every revolution of the piston (even though it fills as a fine mist rather than a formed liquid). When flushing the bottom end of my bikes in the past, I've always used diesel. After getting the diesel to come out clean, I then run a quart of atf type f fluid through it, run it down the street, drain, then repeat about 4 times total, leaving it be on the 5th cycle.
Btw, I've had the same problem with not being able to downshift and after checking everything out, I later realized that I was a dolt and the fix was simply that my shifter was hitting the frame and wasn't traveling far enough to downshift. Just a simple adjustment ended up being what caused my day at the track to end... That was embarrassing, needless to say.