i realize this, and you don't sound dumb at all..in fact you are smart to at least show and ask about your methid here.
checking things like you show in your pictures can produce twice the error you really have if you have one at all.
i did a check on my engines in these pics a week ago and have a more precise setup, but since i am running these engines today i used the test mount to setup a way to show you how things really need to be measured............knowing that not everyone has depth micrometers, calipers and more so a dial indicator as is in the pictures to do exacting checks, you can do a very consistent job of checking by mounting the engine in a solid device to eliminate any movement that will give added false readings. then take a straight edge (the bar from a Robart incidence meter will do) and drill a hole in it, mount it like you would the prop.
starting from one side of the compression stroke with a block up against the str. edge, then rotate it thru to get the other side of the edge to line up with the block you just started with. if that shows a difference, then note it, and then loosen and rotate the straight edge 180 * , retighten and check it again. if the St edge is true you should have the same results........if different, then the straight edge is not straight. get another straight edge and try again.

last but not least is to surface the prop hub, and there is an easy method to do it too.......it just hasn't been posted yet.