im actually in a very similar situation. i was first told i had thyroid problems based on low t3, so i took thyroid meds and that is when i actually spiraled downhill and have been in that low point ever since. i realized later that my initial problem was most likely not of the thyroid just itself but more that the adrenals were stressed, which indirectly put stress on the thyroid.
im no longer on any medications now, just herbs for HPA axis and supplements and an anti-inflammatory diet, but i still have all the classic symptoms of low thyroid AND low adrenal function, so i really have no idea which to address first.
my strategy is to look back to when i first started noticing symptoms and base detective work off of that. for instance, i was super stressed and was having sleep issues, low blood sugar, etc. these are classic adrenal signs.
so for you, i would try to figure out which might have come first, because if the problem originated with your adrenals, it may be best to stop taking thyroid meds and address adrenals.
also, as for it taking 3 years to heal, i would say that it might take that long for someone who is in a very advanced stage of AF. how bad are your symptoms? and what are they?