One problem related to brake pedal and linkage has been reported for the 1999 Jeep Wrangler. The most recently reported issues are listed below.
Vehicle in question was fitted with an automatic transmission. When brakes were applied, brake pedal went below accelerator pedal. If one was not very careful, the accelerator would also be depressed when applying brakes. After the fact, I remedied the situation by affixing a one and a half inch block of aluminum to the brake pedal.