The shift motor on a 2nd Gen Explorer is the LAST thing that needs to be checked. The shift motor has nothing to do with the 4wd engagement on a 2nd gen Explorer. Its sole responsibility is for selecting high or low range. It does not lock the transfer case. Plus, unless they did something up around the transfer case while they were re-gearing it, I highly doubt it's the problem.
The first place I'd look is at the axle speed sensor on the rear diff. When they changed out the gears, they may have disconnected the sensor, or they may have whacked something inside the diff and broken or misaligned the sensor to the tone ring on the differential carrier. The other thing to look at is that they reconnected the wheel speed sensors on the front wheels, although I would think that if one of these was disconnected, the ABS light would be flashing as well.
Without scanning the GEM DTC's there's no way to know for sure what specific fault the system is detecting. If it's nothing obvious (like a disconnected sensor or frayed wires) I'd pay the labor charge to have someone connect it to an NGS and scan the GEM trouble codes. It sucks, but there's no other way to know without guessing.
And, before someone suggests it, no simple code scanner will be able to scan those DTCs. The AutoZones/Checkers/Kragen/Murrays/Napa et. al. scanners will only scan the ECU or PCM DTC's, not the GEM codes.
-Joe
