Could you have a look at the latest public beta build and see if that addresses either of the first two bugs? It’s okay to just run it from the Downloads folder if you don’t want to replace your Applications copy, or to give it another name and have both available—but at this point the beta is if anything more stable than the last release version.
And if not, what is the European keyboard precisely, how is it stated in the Input Sources menu, so I can test it. Is it the one that basically looks exactly like the US-EN layout, but with the € key more accessible? (I don’t know if the Mac even has that one.)
That said, do you mean Option+` instead of Command+`? Because I upon accident discovered that the former 100% crashes Scapple, so does any attempt to insert a “dead key” like that one, into nothing at all. If I have note open for editing it works as expected, though.
As to the rest, you will find all of these points discussed on the forum, and better threads to add any thoughts to as well.