I attempted to just load everything except the xml which contained the National Wonder updates, not understanding any of it,
ummm ... you're going to have to understand some of it!
What I would do with a mod I don't fully understand.
1) Load my mod and the 3rd party mod and make sure they "play together nicely"
2) Merge the 3rd party mod into my own mod, and make sure it all still works.
3) Investigate the 3rd party code to work out how to remove the bits I don't need
4) Remove a few bits that I don't want and retest that I haven't broken anything
5) Based off that knowledge, add a small bit of my own stuff, retest and make sure nothing broke
6) Remove/Add more stuff in chunks, retesting, repeat until everything gone/added
For 4, what you don't want is fairly obvious - the dds files, so search the xml to find out where they are referenced (for say the Great Library) and remove it - just the xml, not the image.
For 5, once the GL no longer shows the splash screen, try making one of your new Nat Wonders show the GL splash, then once that works swap the GL art for your own art, retest.
If you get that working, you should be easily able to swap the rest of the artwork and change the xml for the remaining wonders