I continued to have issues with the rear brakes. The rear disc brake was bending when I braked and I could not figure out how to get it from rubbing on the pads. I eventually took the bike over to REI and paid for a tune-up. Fantastic work by them, the bike has a better top speed by a couple mph now and shifting/braking are much smoother. I was also having issues with the chain jumping off the front derailleur on high torque (high gear from standstill). Looks like I just needed the experts to give it the tune. 

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