A 2" BB will be fine to run your 31" GY MTR's on the stock rims. (most tires measure less than the advertised size)
As far as the lift goes...just go to National and pick up the parts you need.
Here's what I recommend:
- 2" coil spacer + 1" coil spacer (Stack them to achieve 2.5" of lift)
- 1.5" lift shackles
- 1.5" lift blocks
I also recommend Skyjacker Hydro shocks (for 3" lift height) as yours are probably toast anyways and they will be too short for any type of offroad use.
Your total with shocks should be around $550 ($300 W/O the shocks)
Now, the reason I recommend stacking the spacers is this: Most spacers are actually .5" less than the advertised height, ie: 2" is actually 1.75", 1" is actually .75"...you get the point.
Here someting to take into consideration. Because of the year of the Jeep your old springs are going to be very worn out and sagging. Installing a BB will lift your Jeep over the sagged height, not the stock ride height. also, your ride is not as nice as it was when it was new. Installing a full lift kit with new springs will make you XJ drive as good as, or better than, new. Because of this, I personally would go this route:

National 4wd's price: $958.99 + tax and shocks (around $1250 total)
One last thing...expect to break most of your old shock bolts and BE VERY CAREFULL NOT TO BREAK THE REAR UPPER SHOCK BOLTS.,,THEY ARE A PITA IF YOU HAVE TO REPLACE THEM (the nuts are welded to the unibody and often snap off). Spray evry bolt that you need to remove everyday for a week before you start. I recommend using Release All from Canadian Tire...but good old WD40 will be fine.
Hope this helps.