With only 58K miles (before the lift and tires) I broke 5th gear and it locked the shifter into neutral and wouldn't come out.  I had to have it towed home.  I pulled the tranny myself and took it to a shop.  They diagnosed it, replaced 5th gear and replaced all the seals.  It only set me back $300 and a few hours of work.  
One big difference is the number of miles.  Have you considered upgrading to a NV4500?  Some time in the future I plan to upgrade to a NV4500, but I have other priorities for now.  I know a lot of guys upgrade to a NV3550 out of a newer TJ, stronger then the AX-15, but it is still a medium duty transmission.