For your situation: cargo shorts and a merino wool t-shirt. Merino self-cleanses - you could ride for a week in it before getting stinky. I wash both in Nikwax water repellent. This leaves them as capable of ever as "breathing" but makes rain bead and run off them. Merino boxers are a nice touch if you can find them.

SPDs aren't really useful for a commute - the real performance gain is tiny. Try BMX platform pedals instead - they stick to your feet like crazy and let your wear almost any shoe. Stick for the crucial lowest quarter of the pedal stroke is very high, so propulsion efficiency is too.