After my lift I noticed that the leaf springs seem to get lower to the ground and I'm worried that snagging a rock on that bottom leaf will end up jacking my whole ride up. Maybe an Axle flip could do the job... They do it on Jeeps. Could work. What you think?

Yes it can work, however...
There aren't any IFS lifts available to match the rear height once you do the flip.

You then need to be prepared to deal with axle wrap. The lighter springs on the X will tend to wrap when power is applied.

Not sure how much play is available with the slip yolk.

I break off the lower shock mounts pretty frequently, but I wouldn't say it's jacked my ride up.

Aero Steve..I noticed you do alot of extreme offroading with your X and do alot of damage here and there to it...just wondering if your X is your beater upper or is the X your daily driver...

Both, It's never failed to get me home and I have a motorcycle for transportation if it needs to go in the shop. 3 of the 4 shops where I'm a repeat customer are in walking distance of work.

Just avoid the rocks and you won't have any problems.

well that's kind of obvious. i doubt the guy would intentionally uses his leafs as sliders.

in cases where it's unavoidable, it's a sturdy vehicle and i don't think anyone's ever broken a leaf from impact on this board.

Not sure about the slip yoke either, but with the 3" lift my driveline comes within less than 1/4" of the frame crossmember when the rear suspension is fully dropped on both sides. If the springs were over the axle there's no question the driveline and crossmember would meet.

Properly designed maybe not. The spring over Frontiers use a different location for the forward spring perch and a shorter spring. You wouldn't want to do a spring over with the stock Xterra spring, but with the flat Frontier design. For the extra weight of the rear end this would probably be a custom leaf with thicker individual leaves