It is interesting that some of the tests you mention I had done prior to my diagnosis (and vitamin D post-diagnosis).
For at least year before my MS diagnosis, I had a slightly low TSH and a slightly high T4. Then, right in the throes of the neuro symptoms prior to diagnosis, the TSH normalized - waiting for that thyroid result actually delayed me getting a neuro referral because the primary docs thought my symptoms were possibly thyroid-related. A recent test from last fall has been normal. I should check back and see if T4/T3 ratios were run somewhere back in time.
Serum Vitamin D was taken several months post-diagnosis, and after I had started a regular mult-vitamin with about 400 IU vitamin D. My 25-OHD was within "lab normal" range, but based on the vitamin D researchers as in an insufficient range at a little below 20 ng/ml (if I remember the units right). I have no idea what the vitamin D levels were at the time of diagnosis. I have since tried to take more vitamin D on a regular basis, but have not been totally faithful in that effort.