How would I go about editing how many national wonders are allowed per city? Try as I might, I can't seem to find this file.

You can change that by editing the GlobalDefines.xml file.

When you open the file up in notepad, look for this bit of code:

<Define>
<DefineName>MAX_NATIONAL_WONDERS_PER_CITY</DefineName>
<iDefineIntVal>2</iDefineIntVal>
</Define>

You can change the <iDefineIntVal> tag from 2 to whatever you want as the new limit. Or, if you set it to -1, you can have unlimited wonders per city.

You may need to copy and paste the changes into the GlobalDefinesAlt.xml file to make it work. It's been awhile since I've edited that part of the game.