Getting sub-MOA ammo out of an AR is not difficult at all with good ammo and a good barrel. The distances we shoot are not far and that "masks" a lot of ammo/rifle variables.
That said, keep in mind, we're not trying to shoot flys at 100 yards. A 2-3 MOA rifle is plenty accurate for 3-Gun. When I started out, I developed loads looking for the tightest groups at 100. However, after spending the last couple of years shooting long range practical/sniper matches, I prefer predictable impacts over tight groups. Long story short, I use the Dan Newberry Optimum Charge Weight method. It sounds more complicated than it is, and while it's a little tedious up front, the confidence in making a shot and knowing where it's going to hit, is pretty sweet.
As for scopes, like everyone else, check your impact at various powers and at various distances.
Don't obsess on group size too much though. Get a good 200 yard zero (or whatever you prefer) and then practice position shooting from there. At 1.5" at 100, you're roughly 6" at 400, which will cover you for >90% of 3-Gun matches. You're generally shooting at a 12-18" target at that distance, so you're still nailing it with a margin of error.
Rich