You most likely have a late 390 UNLESS
the previous owner just used the block for a service replacement and kept the 352 crank (very unlikely).
This is how I view valuable car modifications (and I am very anal
One can modify the engine if those modifications do not take away from the appearance/value of the car. I would try to find an early unmarked FORD aluminum intake and paint it engine color with a set of stamped FORD rocker covers (painted correct year color or possibly chromed). Maybe a slight camshaft upgrade. One of the worst restrictions on a 58/60 BIRD engine is the exhaust manifolds. An upgrade along with a free flow exhaust will be about the best upgrade you can make.
When I look @ an original car (unmolested) and pop the hood, the theme must be OEM, no STANT radiator caps or INTERSTATE batteries...
But this is your car and you do what you want. I am merely jealous and dreaming with your car...