Update: Mechanic still maintains that disk brakes were intended for mountain bikes originally because wheels get torqued and with disk brakes the cyclist can continue to ride even if the wheel is messed up, meaning that the spokes and rim condition do not normally affect braking. (I am paraphrasing and probably badly.) He did seem to say that there are some spoke issues that could have caused a braking problem. The hop was attributed to perhaps the tire bead not being seated completely. Or maybe the bad rotor.
The fix: A new rotor, because the one installed had a manufacturing defect that caused a little bump or something that was hitting when the wheel went around and caused the brushing sound I heard when pedaling and the very grabby braking action that caused or contributed to my rough and bouncy stops and maybe even the hop as the wheel turned (sounds like a soap opera).
Honestly, I don't know what all caused which problems, but it makes some sense that the defective rotor could have caused the majority of the problems. He did let out the air and make sure the tire was seated properly.
So, for those of you with the basic complete, or a basic with components supplied with the frame, maybe the rotor could be an issue. I think mostly everyone is building their bikes with their own parts. The two guys at this shop, which is a Cruzbike dealership (one of the few in California), also sell trikes and they have had issue with the Clark(s?) rotors before. They replaced mine with an Avid and told me to watch for issues with the front wheel, which so far seems to be fine, leaving me to think that it does not have the same rotor defect. But I will have on my listening ears.
Thanks for the advice and suggestions. I am learning a lot. (And have a lot yet to learn.)