The noise is from the MS suspension. Everyone I know of that has the MS setup has this issue.!!!!! Your springs are in the right place and seating the spring against the perch will not fix the noise. Placing the rubber or silicone in between the upper coils will fix it. Mazda will not admit that its an issue withe the parts. My dealership will not service my car anymore because I kept bringing it back for this (klanking) issue event though they could here the sound too. The springs are progressive rate thats why they are bunched together at the top. Mine look the same. And for the driverside rear of the car being lower, it is even with the stock suspention. Coilovers is the only way to fix that.

I just put the Bilstein HD struts in all 4 corners along with the Racing Beat springs. I can't believe how flawless it drives now. Maybe get rid of those Mazdaspeed springs and get the Racing Beat ones =) /wink