If you're talking a one-or-the-other scenario, in a perfect world there wouldn't be an appreciable difference.
However, in general there can be/is quite a bit of variance in chamber volume from one cylinder to the other in different castings of cylinder heads. I suppose the same holds true for piston-to-deck height clearances, but generally speaking decking and squaring the block will result in a fairly consistent tolerance/clearance value. Generally speaking. If you have a cylinder head that varies across all 4 chambers something to the tune of 2-3ccs, simply cutting the head .020" or .030" may not address the chamber variances at all. Combined with possible piston-to-deck variations on a production shortblock...
Anyhow, I'd build the 460 shortblock or longblock you have. I'd port the lower intake to the heads (either the castings you have or an earlier set of fuelie heads...E7s...with the valves Randy referenced installed) and perform some perfunctory/light port work on both sides of the heads...mainly focusing on bowl cleanups (particularly after installation of larger valves) and cleaning up the exhaust side. Bolt-ons (headers, roller rockers, a good exhaust with a high-flow catalytic converter, adjustable fuel pressure regulator on 24 lb/hr or 30 lb/hr injectors), experimenting with timing, etc., and trying to find a mass-air setup out of a '96 or '97 truck are the easiest mods.
The '96-'97 mass-air setups are worth it. The speed density system was a batch-fire and this is why the fuel injected 302s, 351s and 460s in those trucks never delivered an appreciable increase in efficiency nor power (versus, say, a carbureted version of the same thing produced in the mid '80s) as the fuel tended to start falling out of atomization because an entire bank of injectors all fired at the same time, whether the particular intake valve each was injecting fuel at was opening or not. The '96-'97 mass-air setups are sequential - sending fuel into the intake port only when that intake valve is about to open.
The mass-air setups are going to be more "friendly" to future modifications, as well.
Last edited by Zac; 04-26-2012 at 12:45 PM.