I think you'd be OK starting with the inner cowl panel. That needs to be in place before finalizing the weld to the rocker anyway.
You can also use your floor as a vertical reference as long as you remember to subtract that 11.88" from zero line to floor.
I'm not sure I'd take a chance on assuming the door opening is OK. I fell into that trap and wound up shaving some metal off the edge of one of my doors. I think you can use the belt molding on the door and the cab to establish the opening without removing your bracing (unless absolutely necessary to adjust). Measure down from the belt molding at regular intervals (maybe a foot) on both the door and the cab pillars and then measure horizontally at each of those locations.
Plow carefully.
