Alright, so I finished up my Ex Original Supermap (32k tiles) and have moved on to making the Ext Original x4 maps using the Super Earth. So far so good. I was able to edit the rules and add 4 maps but the game kept wanting to swap out the graphics and units for Sci-fi stuff. No idea why because I didn't use anything from the Sci-Fi folder nor is it saved in a sci-fi folder as I created its own folder. Eventually, I just placed it in the extended original folder which made the maps work great. I did later decide to use the terrain graphics from the orbit of the sci-fi folder and moon terrain graphics from part of the mod database here on civ fanatics. Kept Centaurus the same but changed it from map 2 to map 4. So far so good.
The units though were a real pain in the petunia. Again it kept trying to replace them with sci-fi units despite not having a sci-fi units.bmp in the folder. I switched the files around between the Original and Extended Original folders which seem to reference the original folder. After replacing and customizing the bmp files multiple times and trying to figure out what was going on I finally decided to swap everything out for fantasy units.bmp and then switch them back. Somewhere in that mess, it seems to have sorted itself out but I've really got no idea what was causing the problem or why units were glitching into sci-fi units throughout that whole process. There must be some kind of reference to the sci-fi folder units somewhere in the files but being as I never opened the sci-fi folder during the creation process and I can't find anything in the game folder I really don't know what that was all about. I mention it here in case somebody else experiences the same thing and hopefully my experience can help them.