1) You could save a couple bucks by swapping the mediabridge cables for Monoprice cables.
2) Again, using Monoprice brand vs wiremold would have saved a few bucks.
3) Harmony remotes have been so~so for me in the past, but I have to say the Harmony Ultimate home has been awesome.
4) Any thought to a Roku or Amazon Fire TV?
5) YMMV, but I hate the Samsung remotes.
6)
Will the Audyssey MultEQ XT32 from my AVR-X4000 work just as effectively for tuning with amped speakers as it will with speakers connected directly to the receiver?
Yep. I don't love Audyssey for speakers, but it does do a great job with subs. I have to say I've been able to better it with MiniDSP units, but only with a ton of time and effort, for a result that wasn't head and shoulders "better", but with a little more custom tune.