Don't think I've encountered that problem either. Although, what year do you have? I know the 93 stangs use the same parking brake as the 94 and up whereas the 92 and prior are different.
I had a similar problem with my '95GT. It is lowered with Eibach road race springs (3'' drop). Before I changed the rear shocks to the strange adjustables and bbk isolators, I had a problem with my 1st to 2nd gear shifts slapping the aluminum driveshaft into the underside of the car. It happened several times and scraped the balancing weight off the driveshaft. I cured it with the previously mentioned polyurethane isolators and stiffer shocks. My e-brake cables were not an issue, however.