As long as you're taking the companions, and in this case especially the selenium, all should resolve itself. An enlargement of the thyroid means that the thyroid is trying to mop up as much Iodine
as it can. It means it has been very deficient and is quite desperate to get some. It only does this when it has had enough selenium and when it's save to do so. So, give the thyroid the Iodine
it wants, I'd say.
It will take some time for things to settle. Think months, years. When you're really Iodine
deficient, and you are seeing that your thyroid enlarges to get enough of it, it takes a lot of time to get fully saturated. Your whole body will be deficient. The thyroid will get the first iodine, since thyroid hormone is vital for survival. When the thyroid has had its fill, the other organs will get their chance.
Then, when the iodine comes in, processes need to be rebuilt. In the absence of iodine, processes will fail, one after the other. The body will start up emergency processes, that are not as efficient, but will keep you alive. For instance: you will start using other processes to create ATP, the energy packets, these emergency processes will create only little ATP, leaving you fatigued.
But this takes time. You will no be feeling better within the month, that's just too soon.
Your loose BM, other detox reactions, those will be your lot for the time to come. At some point these will lessen and your BM will become solid again, the zits will fade, etc..
Whenever the detox gets too much, stop the iodine for a day and do salt pushes to get rid of the toxins.
I wouldn't go on a low carb diet. I did once, and I lost a lot of weight on it, but it did nothing for my health.
Food wise, I would focus on what the body needs and adjust my food accordingly. I wouldn't (and do not) concentrate on what to leave out, but on what to put in. Most diets forget the fat soluble vitamins A, D, E, and K2 (MK4). K2 also helps the liver to detox.