Scope cap and adjustment knob tops are not guaranteed to be parallel with the horizontal crosswire in the reticule; nor exactly 90 degrees away from the vertical one. Neither crosswire's guaranteed to be parallel to the adjustment surfaces the inner tube moves across in both horizontal and vertical axes. They're often several MOA off; even a degree or more.
Damn those manufacturing tolerances; someone oughta tell their Mommy on them.
What I would first do, is clamp/anchor the scope in something virtually immovable, then with the reticule center on some distant object, move the elevation knob from limit to limit. Watch that object's relative distance from the vertical reticule line/wire. If the reticule stays fixed in distance to the object, then the vertical knob's adjustment surface is parallel with the vertical reticule wire. Do the same thing in windage with the horizontal wire.
Let us know how this turns out. Then I'll proceed to the next step.
Later. . . . .
Meanwhile, I read through Wheeler's information on that scope leveler. They assume the flat on the scope mounting base is exactly 90 degrees out from the true vertical axis of the rifle its barrel whips in. And also, that the scope's vertical adjustment knob is exactly 90 degrees away from the windage knob's adjustment surfaces it moves the scope across. While they're close, I doubt they're ever perfect. If one's way off, then so will be the end result.