Ok. Back in Feb of this year I installed the Eibach prokit and KYB AGX shocks for my 99 Civic Si. I'm quite sure the problem was there since the first time I put on the shocks.
My right rear tire has more fender gap. More than the driver side. I can get barely one finger in straight on the left side, but the right i can easily get two. It's about 1/2 inch higher.

Well I finally took both shocks out and compared them. They look ok. I completely disassembled the shocks and reassembled them. When they were out I put the springs right next to each other. They were the same height, had the same numbers stamped on them, but the curls in the coil were a bit different. Don't know if it has anything to do with it.

Well I put them back on the car. Drove around to get the springs settled in, and still same thing. To be honest with you I lost track of which side was originally left and which was originally right. I just took a shock and put it in, but I think it was the same as before.

I did have an alignment done a while back, and I did Do it yourself rear camber correction. Problem was there before this though.

Anyone have any ideas what is going on ?! Anything I can do to fix the ride height without sacrificing ride quality?

Basically my rear driver side is lower than the right rear pass side.

 

Is your springs seated correctly? Do you hear popping noises from the higher side?

 

The drivers side(left) on Hondas is always lower then the passenger side (right) due to engine placement and drivers side weight by 0.25" to 0.75". Check your front end and it should also be the same

 

The civics are definitely heavier on the driver's side. Although, your problem might be related to the pro-kit. I have read numerous post saying that their springs didn't 'break in' evenly all the way around. I installed the pro-kit last summer and a month later I noticed the same problem (different heights at different corners).

I'm not sure what to say as a solution except maybe swap sides with the springs if you haven't done that yet and see if that helps. My ground controls will be here sometime this week and that's my solution. I'll just adjust the damn things until it sits evenly. Good luck. Wish I had more of a solution for you.

 

This is a well known problem.

It's called the Honda lean.

There is only one company I know of that compensates for it, and that's Comptech. Their springs have a slightly higher rate on the left side, IIRC.

So, you could custom order some springs that are slightly heavier for the left side, get some Ground Controls, or something, but it's nothing you're going to be able to fix by reinstalling your shocks.

I've got H&R Sports, and KYB AGX's, and I've got the same problem. It's about .25 of an inch off. I don't really care too much. I can't feel any handling problems because of it, and it's hard to see unless you look for it.