I ran into a similar problem on my TR-3650 a few months ago with the Tri-Ax, only mine was hard to get into third. I thought it was the transmission and I was just about to take it to the dealer to have it repaired. I removed the Tri-Ax and put the stock shifter back on and couldn't believe how smoothly it shifted. Then, I knew it wasn't the tranny. I did the following:
1. Put white lithium grease in the black plastic "cup" before snapping it back on the ball of the shifter.
2. Aligned the body of the Tri-Ax with the tranny better and made double sure all the bolts holding it down weren't going to work their way loose (noticed that two were just slightly loose when I removed the Tri-Ax).
3. Made sure the bolts holding the shifter handle to the shifter itself were super tight, as I noticed the bottom one had worked itself somewhat loose when I removed it.
Since then, I've had no issues.