Nice find with the stick shift, I assume it is a four speed? Three speed are even harder to find that four speeds and a 401 doesn't need but three. If that shift boot is original, take good care of it, they are hard to find. Signs it is a real GS: boxed frame, original battery tray on driver's side, Gran Sport on glovebox door, 7/8" front sway bar, never had chrome down the side of the car, did not have halo trim on roof, did have chrome around base of roof like a vinyl top car, rear axle bearings are larger, fender ports are cut through the fender, engine code is L something (I don't remember the GS code, but the L stands for 1965), I believe the four barrel carb was numbered 3922 for a four speed, should have a T-10 cast iron case four speed, and that is all that I can think of now. Of course the exhaust manifolds are specific to the 401 GS as are the motor mounts, but I assume yours are correct because the engine is in the car! That fan shroud (eye brow) on top of your radiator hold down plate is specific to the non A/C GS cars.
Now of course the two fours drastically detract from the value of the car, but I would be glad to help you out there by swapping a stock four barrel straight across!