Just to clarify, the stock is most definately NOT made from American Yellow pine. If you know your rifles origin, this chart :
http://7.62x54r.net/MosinID/MosinSpec.htm (near bottom of page)
should help you identify the type of wood your working with. You need to know the difference between hard and soft wood in order to correctly stain it. You also need to be sure you have finished sanding with the correct grit according to wood type in order to achieve an even looking finish. This is a pretty good video explaining the basics of staining.
http://www.youtube.com/watch?v=9OYMUKkcJyY
Not sure what happened in your case and more information would help. What rifle do you have? Country of origin? Pictures of stock?