And your positive the Flywheel keyway has not sheared as well , correct ?? , something has to have caused the misalignment , not saying that is 100% the cause of the starting issue , but you need to rule things out so you can be sure it is not the cause of the issue
Also , try 1 more starting procedure , just to rule out a fuel issue (make sure it has FRESH Premium first , if the gas is older than 3 months it wont start , and could be a large part of the issue)
Once you have Fresh gas , and have drained ALL the old gas out (disregard if this has already been done) of the tank and carb , then give the throttle 6 full twists , and pull the choke , then slowly push the engine over with your foot , till you feel the compression , then bring the kickstart up till its all the way up , then with all your weight , give a good hard kick , do this up to 4 times kicking like that , it should start by the 4th kick or at least start and die , my 450X requires 6 full squirts and the choke to start cold (with a elect. start) , my R requires no pumps , and a full choke and 4 hard kicks to start cold ...... what i am getting at is sometimes , the starting procedure itself is specific to your bike , what works for 1 bike may not work for yours , and yourself and the prior owner may not have been doing what is needed to start that bike...... not saying this is the case , but its worth ruling out as a cause , since you have pretty much all the components to run , it is getting to the point of being a possible starting procedure , or something (a coil wire unplugged from removing the tank perhaps) that is causing all this , sometimes the simplest things can cause major issues
Try it and report back , running out of ideas
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, if that changes nothing then you may end up having to do as Leardriver said , and cut your losses and take it to the dealer to diagnose , it may end up costing a bit to find the issue , as they have the test equipment that you lack , so they most likely will find the cause , but its going to cost , unless you can get them to "diagnose" without replacing anything , for a set price that is agreeable to you , and unfortunately , none of us can physically be there to witness and go over things to be sure what is what , so we may be missing something , because you did not notice it , as we can only diagnose what you tell us is going on , if you missed something , then so do we .............. But try the starting procedure (including FRESH Premium) and report back , maybe your results will bring something to the surface for us to figure out ...........