'93 Grand Marquis Brake Problem

I have a '93 Grand Marquis LS with ABS and Traction Control.
Last week, the master cylinder and rear brake shoes were replaced when my brake pedal started sinking to the floor (the BRAKE light never came
on - there was always enough brake fluid).
After this work was done, I started noticing that the car would occasionally shudder while moving and the rear left wheel stank like burning brakes. I went back to the mechanic and he replaced the caliper on that side since it was locking up. (I started noticing an occasional shudder a few months ago when driving in stop and go traffic and suspected this was the problem but my previous mechanic said the brakes were fine and my tranny was starting to go (I since moved and am trying out this new mechanic) ).
Smell and shudder are now gone since the caliper replacement. But here's my problem. Now I notice that the brake pedal feels a little squishy under my foot and the car seems to need more force on the pedal to make it stop. Also, the pedal will sometimes sink down a little while the brakes are applied but never down to the floor like it did right before the master cylinder was replaced.
Before I had any of this work done, the brakes were great. The pedal was always firm and far from the floor. I rarely (but did sometimes) noticed the pedal sink under my foot while appied.
My question is: what would cause this to happen? I asked the mechanic since I first noticed it as I drove away from the shop and he said he drove the car and everything is fine. Why would the brakes feel and act differently than they did before?

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