Have you measured the fired case capacity out of the new chamber yet? Should be a little smaller since the gun is tighter.
If I use QL's default setting of 56 grains case capacity, I get a load that's 10% compressed and produces 67,900 psi and 2868 fps. Should be a real cruncher to assemble and a throat burner to shoot. But even at that velocity, for the round to be 2.5" high at both 100 and 200 yards I have to zero at 257 yards and the sight centerline has to be 2.3 inches above the bore centerline, which is way high unless you've got a spotting scope mounted up there. So something is amiss with that information.
If I take the predicted behavior of the 46.3 grain load and look at barrel time and tweak case capacity to land it right on one of Chris Long's Optimum Barrel Time points, it suggests a second sweet spot would appear at around 42.5 or 42.6 grains. Might be interesting to see if that proves to be true.
One other factor is that real ballistic coefficients from real guns often aren't a perfect match to published data. Since your rifle is now shooting pretty tightly, you should be able to safely shoot through a chronograph at 100 yards to record ten velocities to average, then repeat at 200 and use that data with the JBM site's calculators to better get the BC you have with your gun an load. You're kind of getting to that point with the load data where you want some actual velocity data to see what sort of ballistic efficiency you're getting from your gun and how fast your lot of Varget is burning as compared to average so pressures may be better estimated.
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