I've been in college for a few months and I'm having so many problems. Before I got here I sounded almost exactly how I wanted with the style and ease of playing I wanted. I had really good flexibility and upper register tone and fluidity. Then marching band camp came around and since then I havn't been making any progress. I sound like I did a year ago. Another factor may be that i had gingivitis for a while and I'm almost positive my teeth have shifted. (Maybe someone up there just really doesn't want me to play the flute...)
So I've been trying a million different things to unstuff my sound but none of them are working. I don't know if the problem is that I'm not listening closely enough or that my teeth are constantly changing because my gums still bleed on and off (even though I went to the dentist and they said there was nothing wrong with me...ERG.)
I just don't know what to do anymore.

Sorry to hear about your problem. But if you think your teeth have moved or are still moving, you should consult urgently with another dentist.

I do not think it is frequent in young people like you.

Gingivitis is caused by tartar and biofilm accumulation, but it takes lots of time until it becomes serious enough to cause gums injury and loss of bone, leading to the teeth becoming loose. So it could be something else.

The one above has nothing to do with it, you can be sure.

I hope you can get good medical advise and a fast cure for your problem.

I've been using one of those vibrating tooth brushes and they actually do something over time if you use them.
I also mix a solution of a small amount of hydrogen peroxide and mouthwash 50/50% solution with some toothpaste as I brush and I think that this really cuts the germs.

FOr the sound, try recording yourself. nothing fancy, even a computer with a cheapo microphone can help to check the sound/tone quality. Sometimes a recording can be very "revealing".

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Also for the teeth, I always floss when I brush.
That is important.

Of course we who play flutes always work on our tone.

I like the idea of doing the tone studies in between the pieces. This way the tone tends to stay focused more. I think that practicing tone as a warm-up exercise isn't as good because you need to be warmed up to work on your tone.

A brilliant idea!. Warm up with the piece you like most, get enthusiastic (and probably critical with the tone) and then do the exercises.

It may have another advantage: it is easier for me to start practising with the pieces than with exercises. I tend to postpone the practise because I do not like the exercises (somebody does?)

Exercises?
I used to like push-ups but since my gut became huege it made them useless so I stopped. ;-)

Actually what I mean is that I try to warm up a bit, do a piece, focus my tone, play another piece, focus my tone and so forth. Of course these exercise should cover the range of the instrument from middle to top and middle to bottom. The goal eventually is to be able to control every note that we can play.

I read that you just started college and are having these problems. I assume (maybe wrong) that you are around 18 then. Have you had your wisdom teeth removed? I had a problem with insurance and the dentist told me I would be ok to wait the 18 month grace period for oral surgury. Bad idea. my teeth were pushed around and I ended up having a lot of pain and having to get braces (I got invisalign...great idea with flute playing). Just an idea from a personal experience that sounds quite similar.