Flour substitute in Shepherd's Pie?

My favorite flour for thickening purposes is sweet rice (mochi) flour. You can find it from Bob's Red Mill or the Blue Star brand is usually available at Asian grocery stores. It doesn't turn as jelly-like as guar gum, xanthan gum, or agar agar do. Arrowroot is good too, but it's more expensive and less versatile in my opinion.

As for a dredging flour, thirschfeld is right that you don't really need it for a stew. If you must dredge something in flour, I usually use a 1:1 mix of sweet rice flour and one of cornmeal, buckwheat, millet, amaranth, or mesquite, depending on the texture and flavor I'm looking for.

You don't need to coat the meat in anything just brown it without the flour. The only reason for flour is to thicken the sauce. Arrowroot is good but if you heat it for to long, or reheat it to a boil, it will break down. Potato starch is good but if you are making shepard's pie why don't you just use the potato water from cooking the potatoes for the mashed potatoes. Use it as the liquid you add to the meat part of the dish. The water will be plenty starchy and thicken it nicely.

Agar Agar and Arrowroot would be great thickeners. Arrowroot is flavorless and recommended for soups and sauces. Just be careful not to overcook it or you'll have Shepherd's Pie paper mache glue. And Agar Agar is from a sea vegetable and is a product many vegetarian cooks use. Maybe experiment with both? I also recommend trying out an Amaranth flour roux.

As far as dredging flour thats gluten free thats a tricky one; my mother in law and I are both gluten sensitive so I understand the challenge. I would try Buckwheat flour (from the Rhubarb family; no wheat) or testing out some flours such as Rice flour or Amaranth. Since one of the biggest problems in gluten free flours is the fact they lack protein (the gluten) they have problems keeping a structure. So if you add Guar Gum or Xantham gum those are both natural proteins that will help mimic "real bread"(or real flour). Good luck! I'd love to hear what you discover =)

Or you could just skip all this business and buy gluten free flour, Bob's Red Mill makes one. I just am not sure if they added a protein back into it for elasticity.

I did a bit of reading and both cornstarch and potato starch have a tendency to "weep" and lose their thickening properties after awhile. Makes me nervous as the Shepherd's Pie is getting frozen. Any experience? I would love to hear something to the contrary.

Try cornstarch or potato starch.