50000 units is a very big dose. I would suspect the vitamin D was the cause of your problems. If you are sensitive to vitamin D there are many different and smaller dosages available over the counter or online, no prescription is required.
Give yourself a break from vitamin D for a week or two. Then buy some 1000 iU tablets and start with one a day. You can quickly add more if you do okay with one a day. People on this forum often mention taking anywhere from 1000 iU per day up to 10000 iU per day.
If you find out the level of dose you can cope with, then you can buy tablets of the appropriate strength when you've run out of the first bottle. E.g. if you can cope with 5 x 1000 iU per day, then you will save money by buying 5000 iU supplements.
Take vitamin D with your fattiest meal of the day - it's a fat soluble vitamin and this is the best way to absorb it.
The fact that you were prescribed 50000 iU of vitamin D suggests to me that you must be very severely deficient. If you can get your levels up you will feel a lot better.
Regarding the levothyroxine... Since you are hypothyroid you need treatment. It isn't a medical problem you can ignore. Leaving yourself untreated has the potential to cause your body tremendous damage and you will feel terrible. But with the right treatment at the right level you can lead a normal life.