It is close
I like to put the airplane in a level flight attitude, may be just a tad slight tail low. Than set the wheel pants to be level. Than you can temporarily clamp and drop the tail and see the wheel pant gap to ground at the aft tail end. It is not much on the ones I have done, less than an inch, but I like the pants low, may be too low.
I don't have the instructions in front of me but actually that sounds a about right may be a tad high, but it all depends on how high the whole wheel pant is sitting on the tire, ie more/less rubber showing. Following Vans instructions is close but not perfect. If you vary one thing it affects another 3 thing.
Search some more threads on VAF. I remember I posted a thing on how to use string to get more accuracy. To be honest close is good enough about 98%. You really want it to look good frankly in the air and ground. So your eye ball is the final vote. If it looks odd stop.
The wheel pant bottom aft of the tire is pretty close to being parallel to the ground, about the same gap at the tire as at the tail end of the wheel pant. If you follow Vans instructions its close, but it takes some adjustment. If you mount the wheel pant higher up on the tire you will increase the overall gap but also add some drag.
I find the hard part is not getting the wheel pant angle (tail end up or down) but aligning it up side-to-side. That is key. You don't want them toe in or out. That is worse drag wise. The problem with weight on wheels is it changes the gear geometry. So that adds to the complexity but some do it weight on the wheel and I have a hard time seeing where they went wrong.
Some guys do the wheel pants with the engine mount jigged up on a plywood firewall mock-up. It makes measurements so much easier. Basically they make it relative to the plan of the firewall. It is pretty close. So much easier than having a whole plane with wings and stuff in the way. RVator article of old showed this method.
After many years of operations, these wheel pants can take a beating, surprisingly durable. When you take them off, you'll see some scrapes and gouges after a few years. Does not matter you can't see them when they are mounted. They are low for sure. That is why they are low drag.
There are 15 ways to Sunday to mount them. The plans are pretty good but there are so many little tricks I can't think of them all, but eye ball 101 is darn close, with some key measurements.
I would fly with them off at first and get the plane rigged with out them. So when you put the gear leg and wheel pant on, you can tell how it changed the trim.
Again to repeat, if you can get both on and roll it out where you can get a good sight on it, the eye ball will tell you a lot. I can tell you my first pair I went through all kinds of measurements. When it was said and done one was visibly off. I had to plug a hole in the fiberglass and start over. Also as I said consider flying with out them at first, than mount them. You can go ahead and fit them, just leave them off for first few flights to check roll/pitch rigging. The gear leg and wheel pants do affect trim in both roll and pitch.