Luke, It is much easier using a valve spring tester to do it but, really the .060 min. is the total amount of clearance needed over the cams lift. IE all the gaps between coils added together the goal is so that the spring coils don't totally all bottom out at max lift (or stacked) as this would cause bent push rods. You can just install the retainer on the valve stem without the spring to measure the guide seal clearance and also the spring install height using a snap gauge or a like a 6" steel machinists ruler. Sometimes you can also swap the parts around if you find you need a little more for a tight one.
Looking at your direct mount intake it looks like was done fairly well good catch on the cut off stud. That maybe could have been filled in with some epoxy (or better yet welded) and at the two places were is a little narrow not sure there would be any danger of the heat effecting the epoxy that high up on the intake. How did the gasket look any signs of a vacuum leak anywhere?
Looking at your direct mount intake it looks like was done fairly well good catch on the cut off stud. That maybe could have been filled in with some epoxy (or better yet welded) and at the two places were is a little narrow not sure there would be any danger of the heat effecting the epoxy that high up on the intake. How did the gasket look any signs of a vacuum leak anywhere?