Ruger generally mated a .429" (.44 mag) barrel on the Vaqueros, yet the cylinder throats measured .427" (correct for 44/40).
To correct the accuracy issues, Ruger would ream the cylinder throats to match the .429" barrel, and it was a free service.
After that, one could use bullets intended for the .44 special/.44 mag.
I have an older Vaquero in 44/40 caliber, and yes, accuracy does suffer, however, since it's not intended to be used for target accuracy, it's been left as is.
You may want to speak with the Ruger folks, and ask if they still offer the free chamber throat reaming job on older 44/40 Vaqueros.
FWIW: When I was employed, My plant/driver manager had a Ruger #1 rifle in 30-06 caliber, and the accuracy of his rifle was so bad, that it was difficult to hit a paper plate at 100 yards.
After slugging the barrel, it was discovered that Ruger installed a .311" bore barrel on a rifle that should have had a .308" bore barrel.
My guess?
Ruger barreled the rifle with whatever stock they had on the shelf at that time-frame.