The routine thing I do to the Vaqueros and Blackhawks to improve accuracy are:
replace cylinder base pin with a Belt Mountain base pin. It tightens things.
check the barrel forcing cone for concentricity. If it isn't concentric, or is too shallow, recut with an 11 degree Brownell cutter
check the cylinder throats. They are often uneven and undersized. If you plan on doing this a lot, get the reamer from Brownell's. If not, send it to the throatdoctor and he will do it for a modest fee.
That pretty well covers it. Additional things to consider: replace springs with a Brownell spring kit, smooth the action internally, and shoot it a lot to break it in.