Hi, it might be as simple as a ganglion cyst at the toe joint - and the stalk of it has been pressing on a nerve all along. Did you see all the specialists *before* the bump was big enough to be noticed? That can explain why they scanned your back but not the toe. The bump probably is a big clue.
However, a ganglion cyst should not make for a dark area... unless maybe your shoes are very tight, and that's causing around the cyst some minor bleeding. Hard pressing might have even caused the cyst in the first ace.
Hello~I am sorry you are having these issues. Since you have seen all the doctors and the tests are all negative, I would suggest seeing a chiropractor, you perhaps could have some misplaced or pinched vertebrae in your lower back causing this problem. The chiropractor will take some x-rays of the area, study them, and then go over the results with you. If it is something that a chiropractor can help, then he/she will recommend a treatment return, after a few treatments, this situation should clear up and you should feel better.