Just run a new set of Moog replacements, either the cc635 cargo's or the 5665's, will give the rear its stock height back, and make sure they are properly aligned in there stock perches, the springs do NOT sit in just any old position, there are dents to except proper rotation, car will sit uneven if not positioned properly 
Just so you know, my 99 is lowered (not by me, previous owner) and I run 295/35 rear tires on 03 Z06 rims, I had to do some massaging on the inner fender, very minor massaging as they "just" touched, other then that nothing else was needed. 
I thought I might have to roll the fenders like I did on my 92, but was not the case. 
I have been debating swapping in some Moog 5665's in the 99 to get the rear back closer to stock height as I have a small system in the back with two 10's so with the added weight it does not have that muscle car stance I so like
I am not a big fan of them rubber things people stuff in there springs, but my 86 had metal perches that mounted to the rear-end itself and the springs sat on them giving aprox an inch more height.
We put the Moog cc635's in the 96, because every dip in the road or bump and it was always bottoming out after the stereo install, once we swapped out the stock springs and put in the cc635's, never bottomed out again, even when loaded up for the beach
99, lowered, 275/40 fronts and 295/35 rears
96, bones stock springs and height, no stereo, 275/40 all 4 paws, personally I like this old school muscle car stance the best
96, Z06 rims, 265/40 fronts and 295/35 rear tires after stereo install and cc635's rear springs
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