Why has my TSH increased?

This can happen, especially earlier on in the protocol. 

As your body starts producing more Flavin Adenine Dinucleotide and Flavin Mononucleotide, your body starts using up much more T4 and T3 thyroid hormones (because T4 and T3 are required to produce Flavin Adenine Dinucleotide and Flavin Mononucleotide). So then TSH can increase to keep up with the demand.

Your brain is essentially signaling to your thyroid to ramp up the production of thyroid hormone because so much T4 and T3 are being used to produce Flavin Adenine Dinucleotide and Flavin Mononucleotide. This is the most likely scenario because your T4 and T3 look quite good.

It can just take some time for everything to balance out and for TSH and thyroid function to completely normalize, especially as the body uses up a lot of thyroid hormone for the production of Flavin Adenine Dinucleotide and Flavin Mononucleotide.

In the long run, we want TSH to settle somewhere between 1.0 and 2.0. The closer to 1.0, the better. When TSH is above 2.0, it suggests the body is still working on producing an optimal amount of the coenzymes.

Some people need to take more iodine and selenium to support this process. So I would recommend increasing your iodine dosage and selenium dosage. Then retest your thyroid markers again in a few months.

Your TSH should drop back down again over time. It will just take some time to normalize