Welcome to the forum, John. The rods you have are not all that different from a standard 390 rod, and it may be that they were even used in some 390 engines; not sure about that. Normally with an FE you may be concerned with balance if you have a 428 crank, because they were externally balanced with a weight on the flywheel. Since that is not an issue with your crank, external balancing is not an issue. My guess is that you would be fine with all those parts working together.
You didn't mention pistons. What kind do you have? If they are aftermarket pistons, odds are pretty good that the whole assembly was balanced when it was first put together anyway. And if you are going to buy aftermarket pistons, you should have the rotating assembly balanced.
On your block, a 4.13" bore is a standard 428 bore. A lot of 390 blocks were overbored to that dimension, and quite a few of them can't take the overbore. Unless you know your block was an original 428 block, I would make sure to have it sonic checked before you assemble the engine. A 390 block with a lot of core shift, bored to 428 size, could easily blow out a cylinder wall with too much horsepower.
As far as upgrades go, that will depend on how much power you want to make. Do you have a horsepower target?