I'm not real sure what you are asking but if you are asking does it hurt anything to bore to 4.000, it is fine providing the water jackets are not excessively worn.
Is the block babbitt at .010 or are you going to scrape it to proper fitted size?
As far as the oversized intakes, that is fine too but remember that everything works best in combinations. Having the proper camshaft and free-flowing manifolds allows the valves to work more efficiently.