Travis,
I don't see any problems with your technique. As a precaution, you might drill only one of those holes (or both) undersized and peek through them to confirm your alignment before enlarging them. If your layout was off center, you could then make adjustments as you enlarged them. I recently mounted my Freud 1700 VS router to an undrilled JoinTech mounting plate. To work correctly with JoinTech's inserts (much like those offered by Woodpeckers), I had to get the router shaft centered. Even though I carefully made a paper template to use in marking the mounting holes, I did not drill them all at once. Instead I drilled one and mounted the router with a centering mandrel (cone-shaped tip) and compared the point of the mandrel with the center pin hole in the DIY plastic insert supplied with my router plate. Then I checked and remarked the location of the other holes to be drilled. A slight adjustment of some was needed. The base of that Freud router is designed such that ?only one? of the mounting holes go all the way though the aluminum base, and thus you cannot insert a drill bit to use as a marking tool from upper side of the base, and the plastic sub-base did not have accurately registered holes. If you miss your intended centering mark, you could slightly enlarge one or both holes, then use your centering mandrel when mounting your Jasper jig. Please keep in mind that I do not have a Jasper jig. Other members of FOG may have some better ideas. I am not a machinist or expert in how to achieve precise mechanical layouts prior to machining operations.
Dave R.