A 390 is 4.05 bore, 3.78 stroke. That seems to be what you have, yours could be overbored at a rebuild in the past. As for your intake not fitting "right", that's a common thing with FE's. There are so many critical measurements it's easy for a manufacturer to screw up a little on one of them. Most common I've seen is the valve cover surfaces not at the same level as the one on the heads. Usually doesn't matter much, just use silicone for a gasket.