I was able to get the mortises cut last night. I also made a jig for cutting the mortises on the lower back rail using the router since the bottom is not flat and while I have a brace built, this seems easier and gives a cleaner mortise.
Here you can see the blocks I made to keep everything level. Thank goodness for flat torsion box tops!
-- "Do it right the first time, you'll just kick yourself later..."