Man, that glaze scuffing thing hits home. I've seen liners where the stiff brush took off more than it should and the tile looked chewed up after. Feels bad when you think you're doing a good job and you're really just hurting the liner and making extra work for yourself. Good on that Portland guy for stopping and showing you instead of just watching you fight it. Sounds like you had a rough go of it before the switch, glad the softer brush is treating you better.

Did you let it cool down and run it empty for a few minutes to see if the smell fades? That burnt smell is usually the motor windings or the grease getting hot, and a lot of times it survives if you caught it early. The clunking is the bigger worry though, that's probably the gears starting to strip from the double batches. Try running it on speed 2 for 10 minutes with nothing in the bowl and see if it still smells or sounds rough.