Learn about Six O'Clock holds.
If you start off with the minimum published loads, and then work upwards, your P.O.I.'s should start coming down, not up. If you're hitting low, either you're using the wrong weights of bullets, or you're shooting them too fast.
E-mail Ruger and ask them at what range, and for which weight of bullets they regulated this Vaquero for? Its both the weight of the bullets and their time inside the barrel, which causes "muzzle whip". So there must be a really light weight bullet which will always hit low, with any minimum safe loads. From using my old Ruger Blackhawks, as I put a Red Dot on my newest one, I believe that Ruger regulated your revolver's sight for a lot longer range than 15 or 25 yards.
The last time I got to shoot my late brother's 45 Colt New Model Blackhawk at 100 yards, we were loading Trail Boss under 200 gr. Ogee nosed bullets. They seemed to hit a foot low out at 100 yards. And my brother was moaning that they were dropping too much for him. But I had started out the Trail Boss at less than full charges. I was merely trying to introduce him to that case filling sneeze powder.
I was trying to bridge the hot burning pistol powders like Unique, with the dirty ones, such as 2400. Trail Boss, and a light for caliber bullet, (200grs.), seemed to me to be a good alternative. On his big 7.5 inch bbl'd, New Model Blackhawk we had the luxury of adjusting the sights, which you won't have on the Vaquero.
Previously, we used these same Hornady Ogee nosed bullets with hotter loads, (above CAS legal limits), and he was happier with them. But I was sweating him getting a double charge into one of his reloads. But apparently, this was falling on deaf ears.
With any fixed sight six shooter, you can always hold the front sight higher in a six O' Clock hold, to keep your target in sight, pardon the pun. If you grind it down, though, you are going to be like Hiawatha, shooting projectiles into the air, and not knowing where.
Shooting 38 Special Super Police, 200 gr. ammunition, out of a standard, fixed sighted S&W Model 10 with a four inch bbl. will provide a good example of this. Incidently, my old Model 10 S&W was a heavy barrel twin of my Model 58, 41 Magnum. Both of these had non snagging front sights, which were a lot skimpier than your Vaquero's front sight is. So I gravitated to shooting the heaviest available bullets in both of them. This way, the muzzle whip worked for me, instead of against me.
Live and learn!