Look at a number of recent posts about cutting out, stalling, flooding. Almost every one of these problems can be traced back to the stock piece-of-junk vacuum-operated fuel petcock. They just don't last very long and can fail two ways: 1) the diaphram leaks when it should be shut off, or 2) engine vacuum can't hold the diaphram open.
My problem was the latter. Under high fuel use (high speed or driving against headwinds) my bike would slowly run out of gas, as the float bowl couldn't get refilled fast enough.
In your case, it sounds like either a petcock issue (even a new one), a vacuum leak in the fuel plumbing or the plumbing not installed correct.
The best option to solve this is to buy a genuine Yamaha Raptor 660 manual petcock. Don't buy an Ebay Chinese knockoff. Easy to install and foolproof, providing you remember to turn the petcock off when parking and back on before starting.
http://suzukisavage.com/cgi-bin/YaBB.pl?num=1642735417 Edit: if you go with the Raptor, be sure to block off the now-unused vacuum port on the carb.