What do you mean you "attempted" to get the flywheel off ??? , do you have the correct puller ??? and if so did you install it correctly , as you can't tighten the cap down all the way , you can damage the brass end on the crank , and you will lose oiling to the engine
As far as the bucket goes , the shims can stick in the bucket and lift out of the top of the valve spring retainer , if that happens it can slide around , and not go down into where it needs to be , causing a valve to stick open , are you checking the valve lash after installing the tower ?? , you can do so on the bench with the head off , just align the mark on the sprocket with the mark on the tower and check , this will eliminate a valve sticking open as the issue ...... basically , if you have the timing correct , FRESH gas , your air filter connected , your header/muffler on and tight and you have spark ,and fuel to the plug , the bike should run
Have you tried pulling the plug , dipping the electrode tip in gas and reinstalling (dip it all the way till the threads are in the gas) , then try to fire it and see if it pops or fires ???