If you have to take medication for migraine first thing in the morning take your Levothyroxine 2 hours later. Subclinical hypothyroidism simply means that TSH is high with FT4 and FT3 in normal range. Your pharmacist or GP receptionist should give you a medical exemption form to complete so you don't need to pay for prescriptions. You will have to pay until the med exemption card arrives but the pharmacist can give you a form and receipts so you can reclaim costs for prescriptions you have to pay.
The goal of Levothyroxine is to restore the patient to euthyroid status. For most patients that will be when TSH is 0.4 - 1.0 with FT4 in the upper range. FT4 needs to be in the upper range in order that sufficient T3 is converted. Read Treatment Options in thyroiduk.org.uk/tuk/about_... Email firstname.lastname@example.org if you would like a copy of the Pulse article to show your GP.
If Thyroid peroxidase antibodies are high it confirms autoimmune thyroid disease (Hashimoto's). There is no cure for Hashimoto's which causes 90% of hypothyroidism. Levothyroxine treatment is for the low thyroid levels it causes. Many people have found that 100% gluten-free diet is helpful in reducing Hashi flares, symptoms and eventually antibodies.
For maximum absorption Levothyroxine should be taken with water 1 hour before, or 2 hours after, food and drink, 2 hours away from other medication and supplements, and 4 hours away from calcium, iron, vitamin D supplements, magnesium and oestrogen.
It takes 7-10 days for Levothyroxine to be absorbed before it starts working and it will take up to six weeks to feel the full impact of the dose. Symptoms may lag behind good biochemistry by several months.
You should have a follow up thyroid test 6-8 weeks after starting Levothyroxine. Arrange an early morning and fasting (water only) blood draw when TSH is highest, and take Levothyroxine after your blood draw.
Your B12 is very low probably due to your vegetarian diet. Your GP should give you a B12 injection to restore levels but after that you should supplement 1,000mcg methylcobalamin to compensate for the lack of B12 in your diet.