Mark, I wasn't trying to state that the KWs are somehow "better" than other aftermarket coilovers. Certainly, the MCS offerings are true high-end suspension parts and priced accordingly. The KWs are a mid-priced street/track coilover. So my question is, do the KWs have a history of "clunking" in your experience? I have not heard this before, and since I have a set on my Viper it would not be a happy experience to have them making clunking noises (topping out?). I'm still working some of the other rattles out of this car!
Also, all other things being equal, would not the same shock with a slightly softer spring yield a more comfortable ride than it would with a stiffer spring rate? Physics says yes... up to the point of bottoming, of course. Also, I've personally observed the same basic shocks with an isolator and with a Heim joint and the difference in transmitted noise was noticeable-- although admittedly, this was on a BMW M3 and not on a Viper. The Viper uses rubber in its control arm bushings, and in the diff mounting pads, but with no rubber in the shock you have a path for vibration from the lower control arm to the frame. Possibly MCS is damping this path in other ways, but again, an MCS shock with an isolator would likely be quieter than the same shock without.
Another factor is preload. Stock shocks, with their relatively low spring rates (Gen IV Front: 210 lb/in; Rear: 525 lb/in) operate under considerable preload, that is, the spring must be compressed just to mount it on the shock body. The aftermarket coilovers operate with relatively little preload depending on the ride height setting. A "slammed" car will have virtually no preload at all. Preload equals force at zero displacement. You need to overcome that force for the suspension to move, so you have lost small bump compliance to some extent on the stock Viper shocks, translating to lower ride quality compared to aftermarket coilovers.