Problems after deleting Bootcamp Partion/EFI
Quote from OP:


  Now, I think I made the mistake by deleting the Boot folder, but I am not sure. 


My response:

You were correct to remove the Boot folder. 

Quote from OP:


  I would have to shut the computer down, then power up while holding down the option key until I could select the Mac Drive.


My response:

You should have held down the control key before choosing the Mac drive. This will make macOS the default operating system went starting up.

Quote from OP:


  As previously stated, I have deleted everything regarding Windows, so why is the line below appearing?


3:           Windows Recovery                         901.8 MB   disk0s3


My response:

This is part of Windows. You should remove this partition and add the space back to the APFS container. The commands to do this are given below.

diskutil eraseVolume free none disk0s3
diskutil apfs resizeContainer disk0s2 0