I really hate to tell you this...you cut it too short. I count only two threads and part of a third showing. You need to have left at least three full threads. Of course, the way the image is showing...I may be miscounting the threads.
I recommend using the stock brass collet from your TRX Pro or getting a TRAXXAS collet (costs like a buck at the LHS). Get your fly wheel on there. Then give the clutch nut a couple of good hard turns to tighten it down. If you are using an aftermarket collet, it will most likely not grab the flywheel the way you expect and some shims will be necessary. The only collet that I found to work was the TRAXXAS collet.
The other option is to acquire a new shaft and start from scratch...not an answer that you want to hear, but also an option.