RIGHT so there's a couple things for updating people on:
First, the running. I did go to the Running room, as per you guys and also my cousin, and my own suspicions. The shoes I got were VERY freaking expensive ($160!!) but, I like them and I don't feel like I'm fighting them constantly. Apparently I have a fairly straight, neutral gait, which is good, and I also have high arches, so that also means that I need a neutral shoe (because correction either way will screw me up). So, that's what I have. Actually, they're the same as PrpleGrl10's! Brooks Ghost.
I've also done a bunch of research into the feeling of pain I was having, and in particular was tipped off toward tendinitis (which, this early in the game, is not possible, but I entertained the idea of it BECOMING that, as I'm very prone to tendinitis). In particular what I found that there is, in fact, a tendon that attaches to the side of the foot, runs through your ankle, and attaches to the soleus muscle in your calf (I believe). Being that my soleus has probably never had a call to arms like that before, it's probably fairly weak, leading to the major pain. I've taken up doing exercises on my stairs for the poor muscle, and hopefully it'll figure it's life out soon.
On the topic of my knees, and physiotherapy: My knees, both of them, have what's called "patello-femural syndrome," which is considered a sports injury, and was probably from my horseback riding days. In particular, it is caused by my outer quad muscle not being strong enough to pull my patella (the kneecap) over enough and keep it in the right place, so that when I bend my knees and it's in the wrong spot, it and my femur rub together and it's quite painful. The doctor gave me some exercises that actually made me worse, which is why I went to physiotherapy.
The $50 per session, one hour for a session, was actually under my Mum's health care with her work. Otherwise, it would have been a lot more expensive. I couldn't technically even afford that, but my Mum was kind enough to cover it for me. I learned about which muscles, I was given some proper exercises, and have been on my own since.
As of this month, I haven't had any "major" knee pain in almost a year, and I'm really pleased. I've not had to take days off for them, and I haven't been in constant pain for a long time. They twinge now and then, some days they're sore or kind of swollen, but this is far better than what I used to live with.
Thank you for your advice and discussion