Did you ever resolve your issue? I never had the clunking sound, but I experience the horrible, almost unbearable ride after my 3/3 drop using Eibach lowering keys and rear coils. Finally scraped the whole kit and stater over with McGaughy's 2" spindles (reinstall stock keys) and Belltech rear coils. Radically improved my ride, but still looking for a little better ride, so I replaced the shocks with Bilstein 4600s. Surprisingly, my final huge improvement came from the Michelin Defender tires. I love the semi-firm ride I have now, but it's still a little jittery over rough pavement. I know, that to some degree, we expect that with stiffer suspension. I'm now waiting on delivery of new Viking coilovers to see if that gives me the last little improvement. Here are a few things I learned along the way that really affect the ride:
1) Try to retain the original suspension geometry as much as possible. Keys generally do not do that unless you opt for adjustable control arms.
2) You absolutely need to be certain that your parts match (i.e., your shock travel and suspension travel are correct). Bottomed-out shocks are gut-wrenching. But even a slightly wrong shock makes a huge difference in ride quality. Measure, measure, measure. Everything.
3) Make sure to check the bump stops. They need to be trimmed or resized (depending on the level of mods your choose. Free travel mod is absolutely needed in the rear if your lowering and shorter bump stops are needed in the front for most drops.
4) With larger drops, the original Panhard bar offsets the differential about 1/2 or more (to the right side, IIRC). An adjustable panhard will correct that *** tighten up the slop.
5) In many cases, exhausts, e-brake cables, and other dangling things that had plenty of room before, now come in contact with moving suspension parts. This causes all sort of weird noises and may contribute to an unpleasant ride.
6) You can't expect larger wheel-tire combos and lowered suspension to work without some mods. Tire clearance is going to be an issue with most lowered setups. The extent is dependent on how low you go, and the wheel/tire size and offset you choose. The 00-06s really don't have that much room in the wheelhouses for both 22+ wheels and 2+ suspension drops without encountering a little tire rub under certain conditions (full lock turns, or negotiating turns that twist the front and rear suspension in opposing direction, etc.)
Anyway, I hoping you've worked out the issue you were having. Maybe give us an update on what you've found.
