Two years ago, when someone botched a brake job on me (I was expecting pads, and maybe rotors, but it ended up being 4 calipers, a master cylinder, and a warning switch junction too!), I vowed a learn to do all this stuff myself. I subsequently found the Brickboard, and have since done heater motor, trailing arm bushings, struts, etc., and all has gone well.

Today, I took my first shot at brakes - front pads. Followed Bentley; seemed simple enough. Here's some things I did differently:

- after pushing the pistons back to make room for the new pads, I read that you should clean the part of the piston that contacts the shim/pad. I pushed the piston back out by depressing the pedal a bit, but not much happened. I realized I'd have to push a little harder, so I put the old pads back in, to make sure the piston didn't over-extend. I figured it would be the same braking stroke as before starting this job, since the original pads were in. I didn't think about the caveat regarding exceeding the old pedal travel limit on a used master cylinder, which I thought only applied when bleeding brakes, and I hadn't opened the lines. By the time the pistons had pushed out however, the pedal was a lot closer to the floor than before.

- I was careful to keep the silicon grease off of the braking surfaces, but to be sure, I wiped one passenger side pad with brake cleaner on a cloth. I saw that this left a lint on the surface, so I brushed it off with brake cleaner and a brush. I also sprayed brake cleaner on both sides of both rotors at the end, in case there were any grease smears on them.

When finished, Worried now about the pedal travel issue, I did pump the brakes with short strokes to seat the pads. Took her for a test drive, and noticed two problems:

- the pedal seemed really spongy. I also thought it was depressing farther over time, as I was pushing hard, but it never went to the floor or anything.

- at the end of some stops, or when releasing the brake slowly when parked, I got a terrible vibration from the passenger side (low frequency, not a squeal).

Being totally frustrated at this point, I came in to do a post, but then I decided to take it for another extended test drive. At first it seemed a little better, then it pulled to one side, but finally, it seemed to brake quite well. The low frequency vibration went away (although it has now squealed slightly a couple of times from that side), and the pedal does not seem to go down as far now. It does seem spongy, but it might have been like that before I started; maybe I was just focussing on it too much because of the increased travel earlier.

Do you think my master cylinder needs replacing? Is it possible that:

a) crap from pushing in the caliper pistons got into the master cylider seals, but then finally worked itself out (or is there too much brake line length for that to happen)? I've seen recommendations for opening the bleeder when doing this, so the crap goes out instead of back up the lines, but I didn't want to start another possible problem.

or

b) could pressing the pedal past its normal travel once, have gotten the seal dirty, and it cleaned back up over time?

I'm thinking that I should first try doing a brake fluid flush. It needs it anyway, and afterwards with hopefully no spongyness, I should be able to gauge clearly whether the master cylinder seal is leaking at all. The wear-in of vibration and pulling surprised me a bit - or is this normal? Maybe it was due to me wiping the pad with a cloth. Or maybe I put to much silicon on the backs and it squeezed out and got on the braking surface. Would this be "fatal", or would it burn off and be okay?

Any comments or insights are much appreciated.