Prepare the pie crust in advance, hopefully overnight. I chilled the dough for 4 hours and it wasn't ready, so I made the dish the following evening. The dough cooperated much better the second night.
In a large bowl, combine the flour and salt. Cut in shortening until mixture resembles coarse crumbs. Stir in water slowly until mixture forms a ball. Only use as much as you need. Wrap in plastic, and refrigerate overnight, or at least 4-5 hours.
Roll out one of the balls of dough on counter. Set in 9 pie pan and refrigerate until needed.
Saute onions in butter, salt and pepper until tender, not brown. Spread over bottom layer pastry. Sprinkle with cheese.
Blend all remaining ingredients together. Pour over onions and cheese.
Take out the second ball of dough and roll it out for top crust. Be sure to cut slits for venting and secure the top to the bottom by pinching the edges, or use the tongs of a fork to press the top and bottom together.