Black decaffeinated coffee would affect your sugar levels if it is laced with sugar.
As far as VIT D deficiency is concerned,you will have to take VID supplement every week for 8 weeks,followed by once every fortnight for 4 months and then every month for life.
Do take oral calcium suppleement also.
Gradually your levels of VIT D shall be all right.
As far as uncontrolled hypothyroid status is concerned,you must consult your doctor and get the dose revised properly.It can be controlled with regular testing of TSH
,regular visit to your doctor and proper dose of levo thyroxine
Do regular exercises and keep your sugar levels under control by proper diet and regular medicines.
can play havoc with your health later on.
Keep your lipid level in control.
Reduce your calories and be in your required range of BMI.