Swapping big blocks

It would be a manual trans. I do not currently have a flywheel setup. If I bought a neutral flywheel couldn't I have I have it rebalanced later in when I want to use it on the 400 or are the crank bolt patterns different?
Crank flange bolt patterns are the same. I don't know if the flywheel can be re-balanced for the 400 or not, but if you use a stroker kit in the 400, you'll need a neutral flywheel anyway. It's unlikely that the 413 crank is drilled for a pilot bushing, but there are conversion bushings available.