Re: Need help counting clicks.
You might want to start from a bench at 100 yards and get a large poster sized target with a target dot near the bottom and draw a vertical line coming up a good 30+ inches using a plumb bob or level to make it exactly straight up and down.
Then based on your expected come-ups, shoot each 100 yd come-up until you get to at least the necessary MOA for your expected 1,000 yds. ...and, then back down to zero.
At your projected 1,000 yd come-up, you may also want to shoot/verify your expected windage adjustments right and left for 10mph wind based on your bullet's BC.
All that should help accomplish 2 things. (1) you can measure/verify the MOA/click adustments of your scope, and (2) verify that your reticle is straight up and down and that your POI doesn't begin to arc to the right or left.
I'm not sure how much dope you already have on your rifle at various ranges. But, just because the ballistics program says one thing doesn't mean it's exactly right for your rifle.
Hence, all this won't guarantee that you'll be on paper at 1,000yds. You still need to shoot your way out to 1,000yds in 100-200 yard increments or you'll get very frustrated.
Hope this helps!