To clear up a point about Clifford adapters. Clifford sells both a generic 2bbl to 1bbl adapter and the one intended for the Weber 32/36 or 38/38. It just so happens that the Weber adapter fits the Holley 5200 (same bolt pattern). If you purchase the generic adapter (the ont that is not drilled for the manifold), you will be in the same boat as if you purchased the one from Stovebolt. The Weber - Clifford adapter, which is made to mount the Weber / Holley 5200 on the Mustang 6 without the manifold heater comes in two sizes, one for the 1.5" manifold hole and one for the 1.75" hole. If you ordered the generic one you saved a little money but you bought yourself linkage and air cleaner headaches. If you are willing to do this the Stovebolt is cheaper.
Regarding mounting. You can place the carb with the float bowl facing the valve cover, or the passanger fender. The valve cover orientation makes linkage set up easier on the early car (no cable throttle). As for fuel starvation, this issue has been covered many times. If you experience this issue, and not all do, all you need to do is abjust the float level so as to raise the fuel level slightly. Again, not all carbs need to be adjusted after install. Just as not all carbs need to be re-jetted. But adjustment should be on the list of possibilities regardless of the type of carb you get.