What causes pain and swelling in instep of foot?

Possibilities: Sprain/strain, stress fracture, posterior tibial tendon tear or dysfunction or possibly and inflammatory condition such as gout.

Instep: Pain in this area can have a number of cause including plantar faciitis, posterior tibial tendonitis, plantar fibroma, stress fracture , trauma, infection- and that is just the bottom of the foot . See your podiatrist for an evaluation and diagnosis.

NEED FOR SUPPORT!: Most shoes aren't always what is bad, usually it's the crummy insoles they come with! there are many possible reasons that you may have pain in the instep, but try arch supports like spenco polysorb (http://www.Spenco.Com/products/footcare/poly-sorb) and otc anti-inflammatories (like aleve). If these don't help, see a podiatrist.