I've cooked about 20 pies on at least 4 different gas fired barbeque grills. I use a good (dense) 16 inch pizza stone. I've been debating getting a Fibrement stone too.
I start with a cold grill, cover the bottom of the stone in heavy duty foil and then run the burners full hot. I'll end up opening the cover a few times for the first pie to dial in the cook time, as each grill heats differently and factors like a wind can take a lot of the heat out, etc., but I've never tried a stone above the pie. I find that it's very hard to make a pie as good on the barbeque as it is in a home oven. You give up a lot of your ablility to control the heat moving out of your home oven.
I'd suggest using only the bottom stone with the lid closed most of the time, and seeing if you can get the top and bottom to get done together. With the more difficult to control temperature on the grill, you may not be able to achieve a perfect both top and bottom concurrently. I accept this small compromise. I give up a little quality for the convenience of being able to grill for friends away from home. My crust my not have quite the same texture or the cheese may not be perfect, but even a pie we consider "just OK" will amaze our friends.
Withi regard to the uneven burning of the top, was it the placement of the top stone(s), or did it align with your blacksmithing?