I think the only real mechanical difference of '97 v. '99 is the addition of the "multi-mode 4WD" system. However, this change only affected Limited models in '99 and since the 5 spd wasn't available on the LImiteds I assume both 4Runners you're looking at have the basic 4WDemand system. I think the springs were about a half inch higher in '99 and early '00 models compared to the other 3rd gen years. Other than that there were lots of little improvements - see the following from top4runners.com:
1998 :
Several interior modifications, including new audio systems and an additional power outlet in the rear cargo area and coat hooks on the rear seat assist grips, add even more refinement to 4Runner. The 4Runner gets rotary HVAC controls, and revised audio control head units. A lighted, covered passenger-side vanity mirror is now standard equipment on the Limited grade and optional on SR5 models. The 4Runner's steering wheel also features a new, four-spoke design, which is color-keyed on Limited models and black on all other grades.
The Lavender Steel Metallic color was replaced with Cool Steel Metallic.
1999 :
Halfway through the third generation, the 4Runner receives a number of upgrades this year.
New exterior features include a front bumper and valence redesign, new grille treatment, multi-reflector headlamps with an auto-off function, optional projector type integrated fog lamps, new 5-spoke aluminum wheel design for the Limited and Highlander and a few new paint colors.
1999 models feature special UV protection-treated glass on the windshield and front- and rear-door windows, as well as water-repellant glass on the front door and rear window. Inside new features include a new center console/cupholder design improves beverage-carrying capacity, an overhead console with garage door/sunglass holder, two power outlets in the center cluster and an LCD odometer with digital dual trip meters.
A new storage location has been integrated into the rear seats for the headrests when the rear seats are folded forward for additional cargo space. A rear quarter-panel storage area also has been integrated into all 1999 4Runners. SR5 grades now feature as standard heated outside mirrors, cruise control and , built-in map lights in the overhead console .
An option on the SR5 model called the "Highlander" sport package includes color-keyed bumpers with projector fog lamps, fender flares, hood scoop and the newly redesigned Limited 16" 5-spoke aluminum wheels.
4Runner Limited grades receive built-in projector fog lamps, a fully-automatic air conditioner with a digital heater control panel, front power windows with one-touch auto-up/down functions and jam protection (optional in SR5 and 4Runner grades), keyless entry with back window remote and an anti-theft system with engine immobilizer (optional on SR5 and base models).
For 1999, 4Runner Limited models receive a new multi-mode 4WD system as standard. The new multi-mode 4WD feature is actually a full-time all-wheel-drive system with 2WD capability. The all-wheel 4WD mode may be used in normal driving conditions on all types of roads from dry, hard surface roads, such as pavement, to wet, icy or snow-covered roads. Driving with the new multi-mode's all-wheel drive system engaged provides the driver with a more controlled, sure-footed feel to the road because power is applied evenly to all four wheels thus improving traction. To switch from 2WD to the all-wheel 4WD mode, simply reduce the vehicle's speed to less than 62 mph and push in the One-Touch "4WD" button located on the front drive control lever knob (on the transfer case the all-wheel 4WD mode is indicated as "H4"). Returning to the 2WD mode is just as easy, depress the "4WD" button once more and the vehicle is again operating in 2WD.
Off-road enthusiasts will continue to find improved low-traction performance available through a locking rear differential, optional on all four-wheel drive models (except SR5 models equipped with automatic transmission). Sporting a 4.3:1 differential gear ratio, this feature locks the rear wheels together while in low-4WD, forcing both wheels to turn together.
