If I modify a them a lot, how do I change all the 'naming'

Hi,
If I start with a theme, and I make many many modifications to this theme, how do I make certain that I have renamed everything that I need too so that this theme has a name of my own creation. I have no plans on doing anything with this new theme besides use it for myself.

For example the original theme is called your_neattheme.
The functions, for example start like this
your_neattheme_post_nav Using the underscore
And many places in the template files .php files this is also used in the code as well
your-neattheme And using. The dash.

I began finding and replacing all of the original code for instance
your_neattheme and your-neattheme
With
My_neattheme and my-neattheme

When in reloaded the site, then things would not work.
I know that there are many hidden files, files that I can find if I command click on a function and then another file will open up for me to look at.

So what is the process and strategy to rename things.

Thanks.