Sending a thank you letter to a research professor?
Is it too late or &quot;awkward&quot; to send him a handwritten thank you note now that it's been about two months since I've last contacted him?

Nope.
Two months is not so long in the academic sense at all. Whether or not it's handwritten shouldn't matter as much, either. Typing it up is perfectly acceptable, readable, and much easier to correct if you make an error.