by SoCalCruising:
Since you will be decking the block, you will be changing the mounting position of the intake - the intake will sit higher on the heads than with the original deck height. So, when you have the heads on during mock-up, mount the intake with a gasket and torque to about 15 ft/lbs. Check the clearance between the block end rails and the intake surface. There is a chance that the intake will mount flush (no space between block end rails and intake). If this is the case, you must have the intake milled.
Many of us use silicone to seal the end rails and this is especially good if the clearance you have is small (e.g., <0.100"). The cork gasket may sit too proud and not allow the intake to seal against the head if you have little clearance and use the cork gasket. If you have lots of clearance, you can use the cork, plus some silicone to get a good seal.
Ideally, you will mock up the shortblock with at least four pistons - one at each corner. Measure the piston-to-deck height at each corner. This is a good idea because the deck may not be square (i.e., not perfectly parallel to and equidistant from the crank mains). You will want to find the shortest piston-to-deck measurement, tell the machine shop how much you want removed from that height, and then tell them you want the decks squared up on that dimension. Frankly, a zero deck is great, but asking for 0.005" will allow a fudge factor and not affect compression very much