When I make a new resource pack and use a file that has the same name as an existing file from a previous resource, does the new file automatically replace the old file when the user imports the pack?

Presuming the user extracts the files in the same map. The user is asked for it with a question like want overwriting? yes or no.
So don't worry about that. It will be fine.

Just downloaded your image files and they look good. Very promising!

Please make sure to re-download once I take them from "test" to "v1.0".

I'm going to re-explode all of the packs (1-9) and run them against my script to make sure that I didn't miss any, then do some testing and finally publish this script!

I'm really excited to see the user reactions to it. I started 6 months ago by just making some minor adjustments but then really got into it and made a bunch of changes that I think are really good.