Com1 shows in Device manager under "Ports[om&lpt]
Good. There is a physical COM port there. If there were more, they would show up in Device Manager too.
(from your earlier post)
I connected an old serial mouse to the serial port and it worked ok and was recognized in device manager.
If you can still do this, then there is a mouse driver installed that is holding that port open. Avrdude will not be able to talk to it unless you disable that serial mouse driver.
I noticed an unused connection hole...
I believe the holes you are talking about are 'vias'. They are smaller than the holes used for soldering components and are used to connect top-layer traces with bottom-layer traces.