Missed on this combo?

First, the pushrod angle changes as it goes through the lift cycle. The more lift, the more extreme the angle, so there is no magic number to plug into the trig formula. It is usually more than 11*, especially with a roller lifter.
Yes; in this case even if the angle varied from 11* to 15* at the top of the lifter stroke (which I suspect is exaggerated), that increases the pushrod stroke loss by about .003" vs. assuming a constant 11 degree pushrod angle. The point Mike needs to know is that this loss is part of the deal and is not insignificant.

Mike, the way you measured, at the top of the pushrod, would have taken all this into account. So your .409 at the top of the pushrod sounds pretty close to account for the pushrod angle. And you're right, it is hard to get the indicator plunger exactly inline.