Before you pull the trigger on buying wheel parts, take a look at the Wabi Cycles wheelset. It's $150, and might be the best-performing set of affordable wheels out there. Made with double-butted spokes and sealed hubs.

Pedals: since you're on a budget, it's a LOT cheaper to get some BMX-style platform pedals and velcro straps. Track peadls + cages = $$$.