You are absolutely correct Armen.  I have been meaning to get some plasti- gauge and give the vertical clearance a look, but the holiday season has presented too many distractions.  Once the holiday dust settles, I will be taking that reading.  

The vertical alignment would be pretty tough to fix.  I used to work with a product called "Artis Shim Stock" (sic).  It's a plastic shim material that came in a variety of thicknesses.  That might be a possible solution but maintenance would be a total pain.  Another possibility might be brush plating, but it would take forever and also empty your wallet Big Time.  

I suspect that too much vertical clearance would be fairly simple to correct (skim cut the bottom of the cover), but too little vertical clearance would be very difficult to fix.  I'll take the pasti-gauge reading and post the results.

I imagine I should have at least .001" vertical clearance since the spud was around .0015" larger than the cam journals and the cover went home without any trouble.  Anyone know what the actual specification is for the clearance?  Shazam!  I see the all-inclusive Clymer Manual calls it out at .0013" to .0026" with a wear limit of .0059".  Now I've got something to shoot for.

I unearthed this old post to report how the realignment worked.  I've put about 160 miles of hard running on the realigned cover and it is working just fine.  I've run it up to 7K at least four or five times and also did quite a bit of freeway riding.  No hiccups.  I think it's safe to report that this realignment procedure works good.

If you can't find a matched set (head & head cover), you can buy the cover or the head individually and realign them using this procedure.