Hi Nancy - I have Hashimoto's and switched from .137mcg synthroid (levels at dose: TSH 39.48 (!), T3 3.2, T4 18) to NTH in June, when I started low-carbing as well on recommendation of my doctor. I had been on T4 meds for 10 years before the switch and I am 31.
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I switched to Armour and I was on 120mg but the palps got worse.
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Did you plunge right in at 120mg? It takes a while for the spectrum of thyroid hormones in Armour (or whichever NTH you were on) to build up in your body, so if you were getting that extra t3 from the NTH it could release in a rush and give you those palps. Perhaps if you started at a lower dose (1 grain, 60mcg) and stayed there for a couple of weeks, then upped by a 1/2 grain when your hypo symptoms re-emerged, stay at that dose for a week or two (or however long it takes until you feel hypo again) and then up accordingly? Going up too fast is scary - palps suck - but staying too low is demoralizing because you're in perma-hypo mode.
What supplements are you taking? Iodine is something you may want to try out since it's a building block of your thyroid hormones. Google "Lugol's and hypothyroidism" and you'll get a lot of information. I can get my Lugol's OTC in Canada, but I think in the US it's a but trickier - maybe someone else on here could comment on that? Selenium is also supposed to help clear rT3 and I was taking 100 mcg daily until the fall once things were stable with my thyroid, so that could be worth a shot too?
I hope this helps and I hope you find the right medication(s) to better your thyroid - I fully get how frustrating it is to visit doctor after doctor toeing the Synthroid line. You're lucky to have found an open-minded practitioner but like everything else on this forum YMMV, so you'll probably have to continue to experiment a bit before you find the right balance for you. Especially if you're going through the hormonal changes of peri-menopause to boot.
One final Q: did you get your thyroid antibodies tested at your last blood panel? Especially if you're Hashimoto's there may be some underlying allergies (food or otherwise) that are messing you up - mine were over 4000 (the highest my doctor had seen in his 25+ years of practice) until I went GF. I'm getting tested again in March so hopefully they've come down significantly by then.
Good luck! Don't stop researching alternatives (and I second the suggestion to join a Yahoo group or two - there's good info on there) and know that you will eventually find something that clicks.
-Susan