What are the reference ranges for the Free T3 and Free T4, as well as the TPOab? Reference ranges vary from lab to lab and have to come from your own report for adequate comparison.
Both Armour and NatureThroid are desiccated hormones, so I don't understand why your doctor would want to switch. It looks like you need to lower your dose of desiccated, since your Free T3 is high and add a small dose of T4 med in order to increase your Free T4, but changing to NatureThroid isn't going to accomplish that.
Vitamin D deficiency can cause a lot of unwanted symptoms.
Once you post the reference ranges, we'll be able to help more...