Phil, my brain is foggy this morning and I am not sure about the affect of the springs.
I can tell you that I have Eibach springs on my GN which drop the front about 1 inch and my T has regular springs. I just went out and looked at both. Both cars have about a 1/2" clearance from the bottom of the three inch down pipe to the rear ear on the upper control arm.
Looking at them reminded me of something to check, however. Be sure the rear bushing in the passenger side upper control arm is good. If it is worn out which is very common due to the heat from the down pipe cooking the rubber in the bushing, then things can start rattling in a hurry and you will normally notice the sound when driving.
If the engine mounts are worn, the engine will sag down and move around and that usually let the down pipe start banging the control arm under acceleration. Both of my cars have one poly mount on the driver's side and one regular mount on the passenger side.
Also check the transmission mount...if it is bad, it will allow things to touch that should not touch.
The knock against poly mounts used to be possible vibration as the material was too hard so we used just one for street cars. I heard a rumor that someone had developed one with a bit softer poly but Jason, or someone up to date will have to answer that.
Okay, I went and looked. Full Throttle advertises the second gen poly mount which will reportedly handle over a 1000 hp and are reported to be softer and vibration three. They ain't cheap, but, they are forever.
The other thing that can cause problems are worn out body bushings which drop the body down further. That can be seen most likely at the pinch weld that was mentioned above.
If you want the car to drive right, then pop some new springs on it! Worn out, sagging springs do nothing for ride quality and handling.!!
My guess is mounts and body bushings will have the most effect on clearances, springs will be the most noticeable in driving. Bilstein shocks are the way to fly on shocks for best handling and comfort on the road.