Having been involved in putting a '96ish Exploder 5.0/gt40P heads and 89-93 EEC-IV EFI in a 64 Falcon Vert, I can sat that the frame rails are narrower on the Falcon, but the engine bay seems to be a bit longer (ft to rr). We were going to use HIPO manifolds but there was just no way to make them work. Steering box was in the way also, as I recall. Also, being a convertible, working out dual exhaust that wasn't hanging too low was more than the owner wanted to deal with. Ended up using the stock 260 exh manifolds, cross-over, single exhaust. It runs fine and gets very good mileage, so the single exh didn't seem to bother the engine setup.
If you have a 302 in there now, the 5.0 should be a drop-in. And the present exh system, I believe, will mount to the gt40p heads with minimum foolishness. Like I said, we got em mounted with the stock 260 manifolds .