You can get panniers that convert into backpacks. They're very versatile, and maybe an option to consider for your purpose.

I personally prefer clipless pedals with urban shoes. Or you can change footwear when you get to your destination. Of course, the pedals are a personal decision.

As for clothing, merino wool shirts work very well to wick the sweat off your body, thus keeping you cool and fairly dry.

Good luck!