One last test - Start the bike up, let it run for a few seconds, and then shut it off, and pull a couple of plugs. If they are wet, you can be sure that the engine is getting fuel, but the ignition isn't working correctly.
If this is the case, you'll pobably end up taking the bike to the shop, because ignition problems can be rather difficult to find.
It's possible that an injector has failed, and is stuck open. You can test for this by turning the ignition on with the airbox off of the bike. Don't actually start the bike. Open the throttle wide and look down the throttle bodies. If an injector is stuck open, you should see it spraying fuel into the inlet tract. Don't let it spray too much. You've already changed out the gas and plugs, and even though the battery is not a Honda battery, if it has enough power to turn the engine over easily, then it is doing the job.
If you don't already have a manual, download one and review the section that deals with the ign. & FI.
I think it's something simple because you said that the bike ran fine when it was put up. Anybody else have any ideas...............................