Mine was leaking also. I took off the cowl and there is a seal between the air box for the HVAC and the body. I unbolted mine, ran a bead of black silicone and no more leaks. I am not sure if yours is leaking from the same spot or not, but its worth a try.
98 TJ,4.0, 5 SPD, 4' SPRINGS,RC 2.2, SYE W/ TW DRIVE SHAFT, JKS ARMS,JKS ADJ. TRACK BARS, CURRIE ANTIROCK, ACOS ADJ, REAR D44 W/ DISC BRAKES, 62 MM THROTTLE BODY, POISON SPYDER SLIDERS, LED TAIL LIGHTS, K&N INTAKE, THORLEY HEADERS, FLOWMASTER EXH,H4 CONVERSION, 35" BFG AT