As you seem to be aware - the CA model does not have a vented cap, and the tank has a vent hose that is routed through a canister to scavenge the vapors and route them to an extra fitting on the carb....which then routes them into the intake so they can be burned.  If you are ever in doubt about the vacuum causing the fuel flow problem - just loosen the cap and see if the bike will run normal for a few minutes.....it will take several minutes and a few miles before enough vacuum builds up in the fuel tank to disrupt fuel flow.

The stock vacuum petcock is more apt to be the problem, as the vent system seldom causes any problems.  Occasionally a non-CA model will get the vent in the fuel cap clogged.

Thanks guys for the info. When I first rode the '09 CA s40 after I shut it off, I would hear a squeaking sound from the gas cap. I thought it was strange because the '11 model never did that. That is when I thought it might be a vacuum issue in the gas tank. Then I read about the petcock issue and tried to decide which was the culprit.  If I disconnect the tube, then I can put the original gas cap back on and see how it goes. It's been raining the past few days which hampers my troubleshooting. Yeah, I'm an old woose, just getting started on my road riding.
Thanks again, I'll get it resolved and learn a lot along the way.      

I have put the original gas cap (CA) back on and located the tank vent line.The easy place to separate it is under the tank. I could not raise the tank enough to get to it, but I know where it is now. I had not had a failure while using the vented gas cap, however I thought of one other variable that I need to consider if thinking tank vacuum as being the culprit.  A full tank has less open space therefore could determine the time to failure vs a low tank.  So I've found, what I hope, is the likely sources of my problem.There is so much info about the "petcock" that I decided to do the petcock test.  Having the gas cap back to original and the petcock vacuum line plugged (both ways), I went out for my usual short ride.This was another successful run......no problems.  I'll continue. like the test says" to run in that configuration for a tank or two and see what happens.  Thanks to all those who responded or posted info on this forum.  It has been a comfort to have such experience available to me as I learn the s40, alone, here in my garage. We shall see how it goes?
Thanks  AZJim  

You're probably right Justin. Being a newbie at this, I really wanted to know what the true problem is/was.  I'm beginning to think it may be other than what I was thinking. I have not had a failure since I tested it with the other gas cap and now with the vacuum line plugged off. I guess it's possible the carb had some issues. All in all, I'm happy to be making progress, in that it's running pretty well. My goal is to get this problem resolved, then work on the other s40, which is a bit more major.  Jim    

And....be sure to get the proper Yamaha part number  5LP-24500-01-00.  If you are buying it on eBay....don't be suckered into buying a Chinese copy that says "RAPTOR".  If you don't see a photo of a white box with Yamaha printed on it....or they don't state that it is a genuine Yamaha part....don't buy it.

http://www.ebay.com/itm/Genuine-YAMAHA-YFM660R-Raptor-660-FUEL-PETCOCK-GAS-TA...

http://www.ebay.com/itm/Yamaha-5LP-24500-01-00-5LP-24500-01-00-FUEL-thingy-AS...

5sAAOSwGvhT49F9&vxp=mtr" target="_blank">http://www.ebay.com/itm/New-Genuine-Yamaha-2000-2007-TTR90-TTR-90-petcock-fuel-gas-valve-shutoff-/322000021583?hash=item4af8b2684f:g5sAAOSwGvhT49F9&vxp=mtr

Here is an example of a Chinese copy.  (No box...no part number)

http://www.ebay.com/itm/2001-2002-2003-2004-2005-YAMAHA-RAPTOR-660-ATV-FUEL-P...