Get your alignment as you want it and then drill through each end of the intake flange into the head in a safe spot for removable alignment pins. If you use a new 3/16" drill and go into the head 1/8-1/4" deep, you'll be able to use a 3/16" pin for a slip fit to align the intake/gasket/head exactly the same within a thousandth or two, every time. Get the bolts finger tight and then the alignment pins are removed before the bolts are torqued so they don't get caught if there is some deflection. You should only have to do this on one side because the heads are pinned to the block already.
We've done this for decades to make fast change overs on manufacturing machinery, take one module out and pop the other in and the pins save a bunch of work and time. There are other methods and types of pins you can use as well.