BML,
Have you shot your rig at longer ranges? I have a Savage Predator 6.5 Creedmoor that is honestly a 3/4 MOA gun with the occasional 1/2 MOA group at 100 yards.
However, when I took it out on long range steel I fired two 3 shot groups at 960 yards that were both less than 6 inches. It blew my mind! Granted, that was a very small sample size and I will not claim that the rifle will do it every time, but it did it on two different occasions. I've also shot steel at 600 with it a few times and I swear the gun honestly shoots much better at longer ranges and the "flyers" I get at 100 seem to disappear. In a few weeks I hope to go out to the desert and shoot 10 groups at 1k to see what the true accuracy I can expect out of the gun at that range.
Like Boomtube has said, you're probably shooting perfectly within the accuracy limits of the gun and it just looks like you're getting flyers because of the occasional shot that doesn't stack on top of the others. Maybe you'll find something that brings it down to a consistent 1/4 minute gun, but if not 1/2 minute is all the better accuracy that most gunsmiths will guarantee and you got that for a whole lot cheaper
Don't get me wrong, I am thrilled with having .5 MOA that I have been able to repeat several times. I am just pretty new to reloading and it's hard to wrap my mind around the concept that I can shoot two touching but not the third. I automatically assume I'm doing something wrong somewhere in the process.
To answer your question, though, I have not shot long range yet. I am sure I am taking the longest route possible to get to the end, but I really want to make sure that I do every step one at a time so that I learn as much as possible. It's been almost two years developing this load with limited time and dealing with the free bore issue.
My two best groups were .41 with 48g and .47 with 48.5g. I've duplicated both several times. My next set of loads will be in .10g increments between those two. After that, I am going to load 10-12 rounds with the best load and shoot them all through the chrono. Once I do that I am going to shoot long range with my buddy who is a very experienced long range shooter. I know some of these steps I could be doing together, but like I said I just want the piece of mind knowing that I am doing everything right. If that means taking extra steps I am OK with that.