Your halfdoors with the hard uppers will work with the supertop. I have 2 sets of full soft doors. I adjust them by putting only the lower half of the soft door on first. Making any adjustments as needed. Put the other half of the door on, adjust it for the best fit with the windshield angle. See how the door closes, if its tight, youll have to bend the top half of the door outward. If its loose, bend it inward. These are Bestops instructions and I can assure you, I have really put some torque on mine to bend them and ran into no problems. They say in their instructions it may take alot of force to bend them.
If your used to the hard doors as I am, when you put the softdoors on, you might be dissappointed in the fit. They work and keep you dry, but not the best fit. Although after messing with them, for a while, little bend here, little bend there, I think I have them fitting pretty good.