Re: Roofrack info
I am unaware of a factory roof rack. You can verify this with any Ford dealer's service department. You will get better replies by also identifying what it is you will most often be using the rack for; bicycles, skis, extra tire, luggage, etc. Because, there are simply too many possible configurations for prefabricated rack equipment.
My best general recommendation given the obvious desire to preserve the removability of the hardtop is to go with a Yakima (never Thule) "standard" sized basket over the front cab. Go with the longest lateral bars for the application. Then, for the full range of carrying options, mount a front-end hitch receiver and mount the Yakima Goalpost, which will allow boats, skis, luggage carriers, etc. You can go with the existing rear receiver, but it will obstruct the rear tailgate tire carrier and tailgate movement.
Be especially careful with load balancing for any rack setups; Broncos, especially those with lift kits, demand a planned, balanced scheme for putting items above the roof safely. And, if possible, always use a fairing (front spoiler) to reduce wind drag.