has anyone heard of dogs fainting on waking in the morning and seeming inefficient at regulating body heat and it being linked to thyroid conditions

A person/animal who is hypOthyroid will often feel cold to the touch - even tho they don't complain of feeling cold (obviously the animal can't complain ;) ) 
A person/animal who is hypErthyroid will often feel very warm to the touch.
Not sure about the fainting, but hypothyroid condition can make it difficult to wake up and to stay awake.

Hope this helps
Dill