Combining hot melted sugar with cold liquid ingredients
That sounds . . . strange. It would make more sense to heat the milk and sugar together first, thicken with the butter and flour, then add the eggs (tempering them with some of the hot mixture first).

Alternately, you could just mix everything together cold (except for the butter, which would need to be melted). I don't really understand the necessity of pre-cooking some of the ingredients, unless this is supposed to be a "no-bake" pie or something. Enzymes in the eggs will digest the flour unless the mix is brought to a boil first, but I doubt there's enough flour in a pecan pie recipe to really matter (it would take a few days for anything to happen, and I've never seen a pecan pie last that long).