Cone Valve compatibility

Yes they will fit.

Yes, I have 16 black conevalves on my newer ktms, everything fits, fine tune chassis sliding forks up/down in clamps….

What year did the axle size change?

As for length, put the new bike on a stand and put one stock leg and one of the CV legs on and put the axle in with no wheel to compare lengths.  You may need to alter fork height with the CV's to maintain the same bike attitude/balance.

The 2016 Cone Valve is shorter than the stock forks.   Slide the forks down in the triple clamps to adjust.  It works fine but they are shorter.