I've had 3 vehicles with Long Tubes go through DEQ. The only thing that they nail me for is the noise. On my Bronco, I have to unbolt the headers and put baffles in place to quiet things down. Even then, I barely pass, and sometimes don't if they have me in the stall closest to the wall. As soon as I'm home and the pipes cool down, the baffles come out and I'm good for 2 years.
It's easier on the '96+ vehicles. They just plug in and read your computer. Without the sniffer test, they never have you rev up and never realize how loud your vehicle is. My old '98 Cobra was louder than the Bronco, but no problems at all.