I also have a 99 Sahara with a 5 speed. I moved up from 31s to 33s. After going to the larger tires I really noticed the gearing difference both on the street and off road. After about 6 months I regeared from 3.73 to 4.56. Wow, that really made a big difference in how it drove. It's also great the higher clearance from the larger tires. Of all the mods I've done, the larger tires and the regearing has made the most difference in off road capabilities.
99 Sahara - 5 speed
12,500 lb Winch, synthetic winch line, Spyder Front Bumper, Aircraft Lights
Rancho 2.5" Suspension Lift, 1" body lift.
285/75/16 Guard Dogs, Level 8 Alloy Wheels
4.56 Gears, Dana 44 Rear, Spartan Locker in Front, Powertrax No-Slip locker in the rear