Let me start by saying I don't have personal experience here, but I have to agree with Mercury. FE's can be great motors but the 460 should be easier to build and get 500 hp out of. The old rule was one hp per cubic inch. You are 70 closer with the 460. And I think all and all, most people would agree that the 460 build up is cheaper.
If it were me, I would pull the 390 and save it as original. You can always put it back later if you want original. But as long as you are going to modify it, start with the best foundation you can.
Now that being said, I understand the desire to look orginal, and if that is the case, go for it. There is an older book "Ford Performance" by Pat Ganahl that will shed lots of light on the strengths and weaknesses of these engines.
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