i had the same deal as mentioned - seat too low. now i've got one knee that seems to have buggered up cartridge or something.
got a bike fit - raised my seat. no problems now.
- my commuter / coffee shop / beater has platform pedals (but i wear sneakers, not dress shoes. i carry my dress shoes in panniers so i can get a harder work out...)
- Shimano 105 clipless on my road bikes (with a bit of float)

i only get knee pain when i run too far. i miss running too far.
if i was in the same spot as the OP, i think i'd go power strap thingys.