It certainly sounds like you have a good starting point with your current ride. It is true that dual-pivot brakes will stop better than the single-pivot brakes that you currently have. Unless you're going for the lightest or fanciest - and this bike seems more like a easy-riding commuter - Dura-Ace is kinda overkill. Tektro makes nice dual-pivot brakes that will outperform your current set and don't cost too much. And they come in different reaches, which may be necessary on your bike.

The pedals are an easy swap. I have used and like the MKS touring pedals. Be sure to follow the usual advice regarding MKS pedals - when new there really isn't enough grease, so be sure to rebuild them once you get a pair.