Flat Feet with no relief- HELP!

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Hi!
I am a 22 year old female (in the United States) and I have very flat feet. They have been flat my whole life, but I have started having more and more trouble and pain with them in the last few years. I live a pretty active lifestyle (I am not someone who can just stop being active or working out-I guess its in my blood) and I do not want my feet to be a reason I cannot continue to be active. So, I am looking to anyone for help!
The pain in my feet has continuously gotten worse over the last 6 years or so. I always had problems with foot pain, but I don't remember it being so hindering. The first time I really remember having real issues with my feet was my senior year in high school. I ran track and one day my right foot started hurting really bad. I lived with the pain for a while and got my arches and ankle taped everyday before practice. The pain never subsided and my coach thought I could have a stress fracture, so I finally went to the doctor to get an x-ray. Well, the doctors couldn't find anything. They told me there was nothing wrong and they weren't sure why I was in pain, so they just sent me home with no answers and no kind of relief. By this time I had developed some Plantar Fasciitis I think from limping and dragging my foot around school. After a while of trying to do as little as possible (while still participating in my sports) and taping up everyday, the pain finally subsided. Fortunately, I have not had anything like that happen again, but my flat food pain is getting worse everyday.
I am a student-athlete in college and have seen our school's doctor about my feet. He took x-rays to make sure I did not have an accessory navicular bone in either of my feet (and I don't). I was prescribed Physical therapy and custom orthotics (the one's where you put your foot in the mold and send them in) and I have had those for almost 2 years. When I first got the orthotics, I had them in a pair of Nike running shoes and they didn't seem to do much at all. Recently, I have put them in a pair of Brooks running shoes, and they are sometimes very painful. I try to wear them as much as I possibly can to try and help "fix" my feet, but they haven't really helped at all. The part of my arches right under my ankle bone hurts and I also have small lumps (not visible, but I can feel them when I rub my foot) more towards the middle of my arch that hurt really bad-I think they are right where the arch of the orthotic is, so it is pretty painful to walk. I am also noticing that my big toes, especially on my right foot, are starting to turn in and I have pain in that big toe knuckle.
I am having a lot of trouble finding any sort of relief. No shoe seems to help ease the pain. I feel the least amount of pain when I am barefoot; but if I have been on my feet for a long time and I sit down for a few minutes, I have a really hard time getting back on my feet-barefoot or not- because my entire foot aches. I am not sure if this is related in any way, but if I have been walking around or on my feet for a prolonged amount of time the balls of my feet burn so bad I can hardly stand.
I have tried to do research on treatments and remedies, but somehow I always end up at orthotics or foot reconstructive surgery. Well, I already orthotics and the surgery looks terrifying. I guess I am wondering if there is any way the lumps on the bottom of my feet can be shaved down to relieve that pain? or if there is some other kind of treatment or surgery that is way less invasive with a quicker recovery time? I am really not sure what I am looking for, I guess maybe just some insight and help!
I would really appreciate any kind of information or help that anyone could give me! I am starting to get a little desperate!

Thank you!

-girl with a million problems