As you are leaving an hour or more between taking Levothyroxine and drinking coffee there shouldn't be an absorption issue.
I think the symptoms are hypothyroid symptoms rather than Levothyroxine adverse effects. It takes 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. Dose may need adjustment after 6-8 weeks which is why you should have a follow up thyroid test then. Arrange an early morning and fasting (water only) blood draw when TSH is highest, and take Levothyroxine after your blood draw.
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