Yes, use a wooden dowel not a screwdriver. A new pencil would probably do just fine.
While I did mention the possibility of a flywheel sheer, it is a very remote possibility - so I recommend that you don't spend a lot of time on that aspect.
The valves are what you touched and that is where the problem most probably lies. However, it seems you also discovered a potential cam chain failure which, if you had ignored it, would have eventually destroyed the engine.
I think at this point, once you are satisfied with the flywheel bolt, it may be time to pull the clutch cover and take a close look at the tensioner mechanism. If you do, you will need a new clutch cover gasket and a way to remove the old one that doesn't involve using anything made of metal. Metal damages the facings. Of course, the oil must also be drained. If its new, you can reuse it.
Also, the chain should not be skipping teeth if the upper chain guard is there. They can't get over the tooth.
And be forewarned that if the chain is bad, its a major job to change it.
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