for what it's worth, I've installed 2 of these systems on two 2 doors and had similar problems with the clearance off the floor.
What I found was that with the the whole system installed and the flange nuts at the manifold tight, by rotating the over the axle pipe slightly I could adjust somewhat the clearance of the front muffler off the floor. I did find that at the optimum clearance, I had uneven tension on the two doughnut hangers on the mount under the center of the car. Go figure. I lubed the joints with neversieze beforehand, which makes it easier to butch the individual pieces around once its assembled and installed under the car.

I think that the problem has to do with the angle at which the manifold flange is welded to the downpipes. That connection is responsible for determining the path of the pipe(s) [I presume yours is a single downpipe unless you changed your manifold] and essentially determines the closeness of the muffler to the underside of the body.

I found that the rear hanger worked well and located the muffler so that it didn't bang against the gas tank, although it did require hanging the rear muffler from one of the bumper bracket bolts which seemed a little strange.

Otherwise I'm really pleased with this system.