A 9" Ford with a 32" tire has the pinion about 13" off the ground. Danas and 12 bolts will be higher. In a stock front end backhalf car, that has likely been lowered and with the engine and trans in the original location, the front u-joint will likely be lower than the rear. Typically in the stock location, the engine/trans will angle down front to rear about 2 or 3 degrees. In this situation which is very common, in order to make the pinion and tailshaft parallel requires the pinion angle to go positive which you just don't do. It is not unusual in these cars to end up with what is called the "broken back" configuration. Not the optimum set up, but many times you have to compromise and do the best you can with what you have. The alternative is to relocate the engine/trans mounts. If you are building a car ground up, these things are taken into account and positioned correctly, but in a stock bodied, back half car, you usually don't have the luxury of everything being in exactly the right place.
I'm not saying the parallel tailshaft and pinion configuration is wrong, because it is the most correct way to set the driveline up. I'm just saying that sometimes you can't get there and you can't set-up the pinion angle incorrectly to make it happen.
ok when you say the tail is lower, give me an angle on the trans? is the tail pointing up? how many degrees?