I would leave the cali emissions stuff in place for now and concentrate on getting the bike up and running properly. If at a later date you want to remove it, go ahead, but I wouldn't do anything to introduce more possible problems than you have now.
My main purpose of linking that picture was for the hose routing. as you can see, the fuel petcock has 2 hoses running to it. one for the fuel and the other for the vacuum. like I said in my original suggestion, check the vacuum hose to see that's in good shape first and then we can proceed from there.
some other possibilities that you can mull over as we work to fix your bike... any sound plausible?
http://faq.ninja250.org/wiki/Troubleshooting