Would an 8.8 rear axle be a better option to fit in there? I don't have a ton of Ford specific experience; but I know an 8.8 is plenty strong for what you're doing; can have disc brakes, and most seem to have 3.55s or 3.73s from the factory.
I know a lot of guys fall all over the 9"; but, it seems like the answer there is an AFTERMARKET 9" in most cases; to get the brakes, the big ends and etc. that most people want. I know a lot of guys say "well its easier to change ratios, but most of my friends and customers generally dont change ratios often, if at all.