The tests aren't really that accurate (from my reading). And from what I understand, if the test is negative but there's a positive result in symptoms/quality of life, then you should stick with the diet as strongly as any 'celiac'.
We are in this position here. No formal diagnosis but the slightest slip (even a contaminated desk for the children) and mood swings, improper sleep ability, sometimes stomach pain all return (among other things).
If the topomax is giving you grief or has gluten in it, I would guess that it will be very worthwhile for you to change. You might even get better results on some of the meds that didn't work for you previously because your system isn't having to be in constant 'high drive' just dealing with the gluten.
It sounds, to me, like your primary care doc. might just be more in line with your needs than the other one.
I be interested to know what you decide to do and am thrilled that you're feeling so much better already! We too, were amazed at the 'lift' that comes with being gf.