It is not a good idea to get a 331 kit and just drop it in to a used stock block. You should zero deck the block, get the cylinders bored, the main bearing journals checked, new cam bearings along with a magnaflux and sonic check to make sure that the block is good.
The decision has to be how much will it cost to do that work locally, how much is the shortblock, and would you rather trust your local machinist, or the factory machinist.
So it comes down to where the shortblock will be built, if you have a local machinist that you trust, and if you have the measurement equipment to double check all of the tolerances.
I'm not a supercharger expert, but I know that a built 331 is getting close to the limits of the stock block, especially if you spin it higher than 7,000. Adding boost on top of that is pushing it a bit. My advice is to get a main stud girdle and a good harmonic damper. If money is not an issue, get a dart block.