Go somewhere else besides the dealer. The reason they said you'd fail was because they know it came with a 3rd brake light. Go to an independent inspection place where they don't know Jeep's all that well. Worth a shot anyways.
I know it worked for a friend of mine. He had a YJ Body on a TJ frame and they would have had to run an OBDII test on it since it's an 05 TJ really (CEL light is on due to some YJ/TJ modifying). He went to an independent inspection place and they didn't run an OBDII test on it because they thought it was truly was YJ (with coil springs all the way around it lol).
05 Electric Lime Green LJ with a 4spd Auto, 2.5inch Suspension Lift, OME Shocks, OME Steering Stabilizer, 32inch BFG M/T's on 17inch Moab's using Spidertrax Spacers, UCF Aluminum TC Skid, Novak Cable Shifter, Brown Dog MML, Rokmen 1/2 BL, Banks CAI, Diehard Platinum Marine Battery, JW Speaker 8700 LED Head Lights, Safari Nets, G.E.A.R Overhead Console/G.E.A.R Tailgate Storage, Rugged Ridge XHD Front Bumper, Warn Gas Tank Skid, Mopar Rock Crawler Rear Bumper, Warn XD9000i Winch with Warn Wireless Remote, and a Uniden 880 CB Radio