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If you set the Python Executable in Project Properties to the python.exe you want to use then Wing should also remember that one and use it as the default for other projects. Please let me know if that doesn't work as a work-around.
Hopefully that will also address (2) but it would be useful if you can first replicate that status and while it's doing that send us a bug report from the Help menu with the error log included. I suspect Wing is spawning lots of Python processes and the AV is getting bogged down scanning those, but I'm not sure.
I'm not sure why we're not finding the pyenv-provided Pythons and will look into it. Thanks for reporting this problem!