I like the "half-splitting" idea. That might work pretty well since shorter distances are always easier to judge.

Don't worry about what 5 yards looks like for hunting.
Learn what 20 yards looks like, and how far high your bow shoots at 10 yards with your 20 yard pin.
When you get a point blank shot in the woods, you'll have no time to guess, just aim a bit high with your 20 yard pin.

If you already have a rangefinder, use it. Use it to measure yardage to an animal when you can. Use it to measure a few landmarks while in a stationary stand so you can estimate accurately when an animal comes in. Use it all the time, to practice your estimating skill. If your max shot distance is 40 yards, then again just learn 20 and know your drop to 40.
I take that a step further. I'll set a pin at 20 yards, learn how high it shoots midrange, and then set another pin at my max range.

For 3-d shoots, you can go about it two ways depending on your goal.
*If you want to get the highest possible score and have the least chance of damaging or losing an arrow, then have many pins set on your sight and learn to judge very closely.
*If your goal is like mine, you can use a 3-d shoot to TEST your estimating ability and just use a few pins to keep it realistic and similar to a hunting situation.
I don't think there is anything wrong with archery sports for the sole purpose of sport and recreation, but I shoot everything with my hunting setup, and take every shot as if it were real.

Good luck.