A universal joint, or U-joint, connects two rods, allowing them to flex in multiple directions. On your 1999 4Runner SUV, U-joints attach the drive shaft to the differentials and transfer case. Over time, the U-joints wear out and develop movement, which can damage the drive shaft and transmission. If upon inspection you discover a faulty U-joint, you need to replace it. To do so, you will have to remove the drive shafts. When you replace one U-joint, it's a good idea to replace them both, since they tend to wear at about the same rate, and you will have already removed the drive shafts.
Place the 4Runner's transmission in neutral and ensure the parking brake is disengaged. Raise the rear of the vehicle with a jack, and support the rear axles with jack stands.
Place a mark on the drive shaft and the flange where it connects to the differential. You can use a scribe, awl or indelible marker. Make sure the marks are aligned, so you can connect it in the same position to maintain the drive shaft's balance.
Use a socket wrench to remove the four bolts that connect the flange to the rear differential. Attach a cheater bar to the wrench handle to make it easier to loosen the bolts, if necessary. Lower the rear of the drive shaft.
Mark the drive shaft and flange like you did in Step 2, where the shaft enters either the transfer case (four-wheel drive models) or the transmission (2WD models). Remove the bolts attaching the flange to the transfer case or transmission, and lower the drive shaft. On 4WD models, there is an additional drive shaft between the transfer case and the transmission. Follow the previous procedure to remove it.
Remove the snap rings from the four sides of the U-joint using snap ring pliers.
Place the universal joint in a large vise, with a large socket the same size as the outside diameter of the hole on the yoke, against one side, and a smaller socket against the bearing cup on the opposite side. Tighten the vise so the smaller socket forces the bearing cup out of the yoke, into the large diameter socket. Use vise grips to finish removing the bearing cup.
Reverse the position of the sockets, and repeat the procedure to remove the opposite bearing cup. Reposition the U-joint in the vise to repeat the procedure on the other axis of the U-joint to remove the bearing cups from the drive shaft. In total, there are four bearing cups you must force out, two each on the yoke and drive shaft.
