Just purchased my first Samurai.  I'm coming from the dirtbike world, so forgive my current ignorance. 

-Stock 88 Samurai I'm building up for a lightweight, go anywhere camper.  This vehicle will be used around Utah where I live.  Not serious rock crawling, just be-bopping around with my wife and son in the Canyonlands, etc.

I'm putting 31" tires, 4.9:1  transfer case, and I'd like to put an affordable mini-spool on the rear.  My question is, for comparitively mild wheeling, will the stock axles be fine with 31" tires and a rear mini-spool?

Thanks in advance.
 

You should be fine as long as you don't pinch the tires in some rocks.  I ran 33" tires for years before I finally broke an axle, but I have seen friends with 31" tires break one or two axles a year.

For driving around I would recommend a locker instead of a mini-spool.  The spool is going to put a lot more wear and tear on your rear axles then a locker, especially on pavement.  Every time you go around a corner you are basically dragging a tire.  It's an extra 100 dollars but worth it in the long run.