Before you go pulling anything apart, check to make sure you have the retaining clips in properly.

My brakes started to "chatter" and make vibrations so I bought all the parts to replace them. But when I went to change them I notice that the retaining clip on the driver side has popped out on the bottem.

Yeah good point. Man, putting those things back on are a PITA. No, those are on right. Its not the chattering, its more of a vibration (only breaking at speeds over 50mph). It drives me crazy.

Question: If I turn the rotors, will the slight wear in the pads be a problem with bedding to the new flat surface? And if so, would it affect breaking performance?

more than likely the rotors were not flat and true to start with, either that or you have a bad wheel bearing allowing the rotor to "wobble"

don't worry about the pad wear; go ahead and get the rotors turned but cut as little as possible, and get them turned ON the car if at all possible, you will end up with a truer rotor in practice.

Next time, buy a quality rotor.

Is it worth it to turn them while they are on the car? The guy down the road charges $5 ea to turn them if I bring them in. Around here only the dealer can turn the rotors on the car, which they would charge quite a bit more at $75 per hour.

Either lathe, on the car or off the car, can do a quality job if the equipment is good and the machinist knows what he is doing. The on the car can be better, but I don't think I would pay the difference for a home brake job.

yeah, in your case, its probably not worth paying for the on-car turning.

Ah my favorite topic or that which haunts me the most! brake shudder or TV thickness variation.
http://www.bendixbrakes.com/downloads/Twenty-first-Century-Rotors.pdf and the many article on www.stoptech.com

Since this happens to my Mystique on a regular basis, I just tried a experiment. First I'm have Stazi's rotors and just found out 1st generation Bendix Titanium's with approx 20K+ miles. I used a 6" right angle random orbit sander to clean up the rotors. With 180 grit I knew it wouldn't remove that much. Jacked up one side with motor at idle (ATX) D or R cleaned both sides of both rotors. Cough cough got to remember, buy more dust masks!
Installed torqued and headed out on the back country roads and did 15-25 hard stops from approx. 60-70mph down 10-20 mph and continued on allowing several minutes or so cooling. The key is not to stop and allow the pads to imprint on the smoking hot rotor. So I've read on the Bendix site and Stoptech.com site. Not the easiest process to finish without traffic causing interruptions. This is first time I've tried this lengthy bedding process. If the burning of the eyes the next morning opening the garage door is any indication, I believe I managed to transfer a good even layer of pad materiel to the rotors. Actually the deep dark bluish rotors with a slight tinge of gray is what I was going for.
I'll see how long this the smooth pedal lasts. I think this is where the proper pad material comes into play? But since this chassis invites aggressive driving ever so often, possibility not possible to design any pad material for such a wide range?????
I'm thinking majority driving with many easy stops is reducing transferred pad material and eventually becomes uneven???
I'm thinking maybe I should replace the slider pin bushings? Original calipers 98 Mystique LS (07/97) Brake fluid flushed many times with Castrol LMA. Lost count, I have a bad habit of forgetting to write that in my maintenance log. The pistons are still nice smooth operation.
How many have noticed the light rust layer on rotors after washing ? This may the start lead to the unevenness, also?
So many things to try so little of a budget!
TNX
Paul

I had the rotors turned and it improved the shudder at high speeds quite a bit. I guess that the cheap rotors sometimes require turning prior to using them.