Picture tells me its a 69 390 Car and its not concours.How Ford did it is not important.I agree on having the manifold surfaced but that's only one half of the sealing surface.Depending on how long it has been leaking the head may need surfacing as well.You may spend two days fixing it only to have it blow the silicone out in two weeks and be leaking again.Silicone is a short term band aid when it comes to exhaust.
I would simply yank the engine out.It will take less time (and pain) that trying to fix it in the car.Chances are some of the top bolts are sized or will break..Then what
.4spd cars are a pain I understand that....
McCord makes a really nice proper exhaust manifold gasket for your application.Not header gasket stuff.I am not saying to use them but if the head is damaged you only have two options.
I am a machine fitter by trade and in no way apposed to a gasket less surface but things have to be right.At least if the engine is out you can draw file the cyl head.
I am not one for taking chances or gambling.....JMO....Cory