Do you take all of your Armour in one dose or do you split it into multiple doses throughout the day? Most of us on a T3 med find that splitting the dose works better than taking it all at once. For instance, I'm on 88 Tirosint and 10 generic T3... I take the Tirosint in the morning, with 5 mcg T3 and the other 5 mcg T3 around noon.
Your doctor is almost doubling your dosage and I think that's too much. Because Tirosint is dissolved and absorbed much better than pill type meds, many people have to start out on less, rather than more. 25 mcg cytomel is also a pretty hefty starting dose.
If you do make switch to Tirosint I'd love to hear an update on how you're feeling. I've been wanting to try it.
The change from alternating 90mg/120mg of Armour to 125 mcg Tirosint and 25 mcg Cytomel actually represents a considerable increase in both T4 and T3. The Armour you've been taking contains roughly 65 mcg of T4 and 16 mcg of T3 per day. The conversion chart assumes, as you thought, that you're replacing the Armour with Tirosint alone. If you're adding in T3 at the same time, the chart doesn't work.
Do you have your lab results to post? Please include reference ranges as they vary lab to lab. I can comment on your last question better after seeing you labs.