" However its only rated at 100 watts rms and the Dynes are rated at 400 watts. I felt guilty not providing them with more power from a more modern amp."
There's no standard for measuring watts. So if you take 10 different amps all rated at 100 watts/channel and measure them the same, every one of them will put out a different amount of power. Also, you may not be reading the specs right with regards to the speakers needing 400 watts. Its probably for transients, not continuous. The easiest way to tell if you need more power is to do some listening. If the amp is straining, you'll hear it.
" Would i get a noticeable difference and or warmer sound with the ref5se?"
There's no way to tell without trying it. If you are looking for a more traditional, classic sounding preamp, ARC is probably not the best choice.
"Would you guys still recommend using wyred DAC to connect to ref5se?"
Any answer you get on that will just be a guess.
"Im thinking it makes more sense to upgrade 1 component at a time so it's easier to hear the difference. Any thoughts appreciated. "
It sounds like a good idea, but its really not a plan for success. There's a huge difference between buying components and building a system. Can you name a system in your price range that you would be happy with?
