Can you have TSH [1.09] and t free[o.66] which are within normal parameters and still have low thyroid function?

No. If your TSH and free T4 levels are normal, you do not have low thyroid function. However, a free T4 of 0.66 would be low in most labs. Low free T4 with a normal TSH could indicate a pituitary problem.
Thyroid. Not usually. Why do you ask? What are your problems? Have you considered that you may also be vitamin d deficient?