Just a few thoughts on things to check: did you pre-heat your baking stone for an hour? Many of them take that long to come up to temperature. Did you happen to take the internal temp when the pie was finished baking (165F in the center)?
Assuming neither of those caused a problem, you could consider brushing a thin layer of melted clarified butter over the bottom and sides of the cold, chilled bottom crust (but avoid the edge where the two crusts will be joined). When that film of butter is firm, then pour in the filling, add the top crust and chill for an hour before baking. While firm, the butter will moisture-proof the crust, but then as the pie bakes it will melt and mix with the filling (a touch of butter goes well with lemon, no?).
The other thing you could consider is to make an open-face pie and replace the top crust with pastry cutouts. That would allow you to blind bake and moisture-proof (with egg white) the bottom crust before you fill it. And the cut-outs can be baked separately on a sheet pan and then placed on top near serving time. This is a method I use a lot For directions, take a look at the cherry designer pie or the open-faced designer apple pie.
Good luck, sounds like a nice pie!