On my stock '94 with Eibach springs and Tokico blue shocks, I'm also seeing about a 3/4 to full inch of extra height in the rear. I, unfortunately, do not have a supercharger to weigh my front end down, so I can't attribute this to anything other than my lack of spare tire, which I don't think would have THAT much effect on the ride height. Let me know how much you end up cutting off the rear springs, because I'd like to do the same in order to achieve a more uniform look.
'07 Toyota FJ Cruiser
(Sold)1997 Lincoln Mark VIII LSC Black/Black
Chrome Cobra R's, BFG Rubber, Cobra/KVR Brakes
Custom Koni front air struts, Bilstein/Addco in rear
Cobra Intake Manifold, SCT XCal by Lonnie of BOC