Provided the tab in front is still in place and not rusted away it is actually difficult to install the seal incorrectly. Now if the tab is gone then you have a puzzle. Anyway the first photo should explain the correct orientation.
Since the hard top can pivot at the B- pillar locking handle the rear can go up if the front comes down too low. In that case the door window would not roll up completely provided you did not make any door window adjustments. Have you checked that?
The only way you can raise the front is by adding shims under the locking screw on the hard top. They are shown here:
http://www.sl113.org/forums/index.php?topic=17760.msg123375#msg123375.
Another possibility for the raised rear end is an incomplete down lock of the B-pillar handle. The left and right handles are not identical and the pin is not exactly perpendicular to the handle. Make sure these orientations are correct. See second photo.
Also, if the hex nut is not flush with the bushing through which the handle stem goes than the cone shaped assembly cannot be seated deep enough.
Finally, if the chrome cap over the B-Pillar is installed too high - I imagine that this is quite difficult to do - then the top would ride to high.
Hope this helps identifying your problem.
And yes, the plug shown in the previous photo faces down. It goes into the bottom of the hard top right next to the U-channel seal.