Well, remember, everyone has a different experience with these things. Here's the magnesium story -- Vitamin D helps calcium get absorbed better. Calcium and magnesium are in balance in the body, and too much calcium can leach magnesium out of the body (just as too much magnesium can leach calcium out of the body). The recommended daily amount of Vitamin D is 800 I.U., but some docs and natural physicians believe in very high doses if certain conditions exist. I have no idea what you were taking this for, but if was just for maintenance, you were taking way too much D. Keep in mind that most Americans get too much calcium and not enough magnesium in their diet. The main reason for this is the excessive consumption of dairy -- dairy is very high in calcium but deficient in magnesium. The best sources for magnesium are green leafy vegetables (also the best sources for the proper forms and amounts of calcium) but most Americans don't care much for them. So say with bone density, the bigger problems is magnesium deficiency, not calcium deficiency, but the milk lobby is huge and the leafy green vegetable lobby isn't. Most people have a hard time digesting dairy -- it is, after all, intended only until weaning, and that's human milk. Cows are quite weird in their way of digesting foods and they were created by humans, not evolution. If you get out in the sun for a half hour a day at peak hours, you probably don't need any D supplementation, but most of us don't do that anymore. As for the B6, it's probably your culprit, but keep in mind, magnesium deficiency can also cause some of what you're describing. I have no idea what your diet is like, but a balanced B complex would have solved this problem. The other problem is that B6 is in balance with B12 and folate, so you might be deficient now in those. Not to be snarky, but your doctor doesn't sound very knowledgeable about this, which is typical of docs in general. A holistic nutritionist might have been a better fit. A couple years ago the gov't reduced recommended supplementation of D from 1000 a day to 800 because some people were having bad reactions from taking too much. There are situations where this is a useful treatment despite risk, such as a lot of overall pain, but not for an otherwise healthy person. Also know that only D3 is the form humans use, so I hope your doc didn't put you on a synthetic form that the body can't use well. It's good, though, that you're getting better, and in the future if you want to use supplements, buy them already balanced by highly reputable companies found only in the best health foods stores. But be careful if you ever take a lot of supplements -- some companies have a tendency to put B6 in everything. Good luck.
Have you considered transdermal CO2 therapy in lieu of some supplements to boost your blood flow?