I can't imagine what valves or throttle bodies can have anything to do with his problem. Especially disturbing is the fact that it gets worse when the bike is hot.
There are only two choices here since the battery is fine and it cranks good - either spark is missing, or you got fuel delivery problems. I would rule out the absence of spark because at least some cylinders would fire, and the engine would start although having abrupt and unstable rpm for a few moments. If the engine sounds fine once it starts, then it doesn't look like you have a problem with the spark. There is a remote possibility that ECU doesn't send a signal to spark plugs because it is defective or because of some defective sensor.
That leaves the fuel issue. Partially clogged injectors can do that. If the bike runs fine at higher rpm (requiring lots of fuel), I would rule out clogged fuel line/fuel pump issues. So, I would put a quality fuel cleaner per their instructions - use only Sea Foam, or Red Line, or Techron. Most everything else is junk. Also, if you crank for a few seconds and it doesn't start - stop cranking and run to the exhause and smell it. If you don't smell any gas, this means the gas was not injected into the combustion chamber.
Are you getting any codes? Do you hear the fuel pump prime once you turn the key to ON? If it doesn't and only starts working when you are cranking, there is not enough fuel pressure in the lines to push the fuel through the injectors, and it takes a couple of seconds to build it up.
You could certainly pull the plugs and take a look if they look fine. You can also test that the fule pump moves enough fuel by disconnecting the line going to injectors, putting it in some sort of a container and trying to turn the key to ON. In a few seconds it should produce more than an ounce of fuel.
I personally had exactly the same problem with a car - would crank excessively before it starts - especially in the morning. Put the bottle of Techron in, and the issue is GONE! Starts pretty quick.
Pay attention where you are getting gas. If you are getting mostly in the same place, I would research their quality of gas. Also, try using Shell gas stations. Their gas is a bit more expensive, but they have cleaning additives and no junk in their gas - well worth the extra $$.
Please let us know what you discover. But be consistent - that's the only way to draw logical conclusions.
