Yes, it's always good to test antibodies, both TG and TPO. Ferritin is the storage protein for iron and even if your serum iron levels seem fine, ferritin is the one that really matters and it tends to be low with us often. You want ferritin to be in the 70-90 range.
I'd recheck the protein levels just to be sure. They can go up if you have inflammation of some sort going on and that may be what was happening. And if you can't easily ask your doc questions without him getting defensive then you need to find one who has better people skills.