It takes approximately 4-6 weeks for a T4 dosage to take full effect, so it's not surprising that your FT4 level hasn't increased since you started taking it. It's also common for symptoms to get worse for a short time before they get better when changing meds or dosages. I've never had the type of pain you're referring to in the leg unless it would be classified as cramps. That could be caused by a number of things, other than Synthroid - one of the main things that cause cramps is magnesium deficiency, but if it's not cramps, I'd hesitate to say what it was.
You might have started on too high a dose of Synthroid and you can try splitting it in half for a week or so to let your body acclimate to the medication, then try increasing or you can ask your doctor for a different medication, such as Levoxyl, which is typically tolerated very well. This would probably be my choice.
There will also be some conversion of Free T4 to Free T3, so you may have to adjust your Armour further, as well.
What were your thyroid meds and dosages before the change? Do you split your Armour dosage and take some in the morning and the rest in the afternoon? Did you defer your morning meds until after the blood draw for those tests?
Since you took your Armour dosage 4-5 hours before blood draw, your Free T3 result does not accurately reflect your actual level. The same applies to your Free T4 but to a lesser degree. An excellent thyroid doctor has recommended that a patient taking adequate NDT will have FT4 around the middle of the range and FT3 in the high end of the range . Since you mentioned that you were feeling pretty well at that dosage, It seems to me that the first thing you need to do is to get new tests with your morning dosage deferred until the blood draw. That will give you a better estimate of your actual levels. Then if you think you need to raise your FT4 you can add some T4 med. If you need to raise both FT4 and FT3 then you could just increase your Armour.
Also, your B12 would be better in the upper end of the range, and ferritin needs to be at least 100. A good supplement for ferritin would be Vitron C, since it contains some Vitamin C to prevent stomach distress from the iron.
Personally I would not want to switch to T4 med only because of the usual problem of inadequate conversion of T4 to T3. Since Symptoms can be shown to be directly related to FT3 levels you need to assure FT3 in the upper end of its range.
Some people have no problem with taking it all at once. I split my dosage in half just to avoid some of the issues you mentioned. I think it is the best way to go and my impression is that most hypo patients do that.