Pain behind ankle(Medial) + fallen arch. Can you help?

Generally, arches do not fall, but asymmetry is something you are born with. It sounds like you overpronate on the right side (foot turns out and falls in). If you are thinking of taping while running in vibram shoes, you may end up with blisters from friction and movement in the shoe.

My guess based on what you are telling me is that the soft tissues on the medial side of the deep calf into the posterior knee are tight from turning out and you are hitting hard on the right side vs the left.

The easiest way to help shimmy that up (level you out) is to wear a minimalist shoe with an off the shelf orthotic such as superfeet which will work well in those. While it is not like running in Vibrams, it may be what you need.

Pure minimalist is not for everyone, and some folks need alittle help. I think you may fit in that group.

It may also be a good idea to find a good sports chiropractor who does extremity work and understands running and runners. Ankle manipulation, myofascial release and some core work can markedly improve your running experience if you find the right doctor.

I hope that helps