I'm unaware of your particular version of the Ruger Vaquero. Ruger revised their Y2001 catalog to include their "Sheriff's Model" which has a 3.75" barrel, birdshead grip frame, and black macarter grips. This version is available in either blue or stainless. During the past 2 months I've obtained 2 of these, both in stainless.
However, on a business trip to Birmingham (AL), I saw a Ruger Vaquero with what appeared to by a 3.5" barrel. (The retail dealer was Southeast Gun in Centerpoint and the price was less that what I paid for my Vaquero Sheriff's Models!) The gun was stainless steel and had ivory type grips. But, unlike my guns, it did not have the birdhead grip frame. I presume this must be what you have (?). Some of the big distributors (Davidson's, AcuSport, et.al.) are getting limited productions variations made by Ruger.
In my humble opinion, I would not hesitate to shoot it. Seems like there is an increasing number of "limited edition" models being added and this will not inhance the value of any of them. Winchester is an example of this and they used a zillion versions of "limited production" models to provide financial liquidity and "postpone" ultimate bankruptcy.
Enjoy your Ruger!