Running Shoe Help!!!

It's a misnomer that flat feet require intervention. Take a look at the studies that have been done on stability shoes and biomechanics. There's little evidence such shoes provide any benefit. Stability shoes could potentially be injurious. Same for aftermarket 'orthotic' inserts.

Btw, I also have flat feet and tried a pair of Vongos a few years ago. Instant knee pain. The shoe's stability design, particularly the medial varus angle, caused my flat feet to roll to the outside. This led to medial knee pain behind the patella.

My experience is that shoes with too much support/motion control will irritate my IT band (outside of the knee). Interior or front knee pain would be more likely with shoes that don't have enough support. For knee and back issues, you probably have some weakness or imbalance. Try to find a good sports PT for an evaluation.

For foot pain on the bottom, I would be thinking plantar fasciitis. If pain is in the forefoot, then your shoes may be too narrow in the toe box - maybe as a result of the new insole. In either case, for foot pain I would consider a change in shoes.

My husband is flat footed and likes to go the minimalist shoe route, specifically with Vibrams Five-Finger. It seems like a lot of these ultra supportive shoes are more of just a crutch than a help. If you go the minimalist route your feet will actually be able to naturally build strength rather than need to rely on shoe supports. That being said, he also has a pair of Brooks Beasts that he says take away any foot pain he feels when he runs, so you could check those out too if you really want a supportive shoe. Those are made for heavy pronators though, so they might be overkill if you only pronate slightly.