So I tried re-installing the mod in its entirety, but the same issue occurs with the units: for whatever reason, the ships (excluding submarines) and mechanical land units are all sticking front first into the ground/ocean. I'm unsure how to just redo the common folder part of the installation (what rhettrongun suggested), though I feel like the complete deletion and then re-install should have fixed it if the problem was with how it installed. any ideas?
If you repreformed the entire installation then any issue with the common folder would have been corrected. So, the problem lies elsewhere. I'm not really sure though, as this is something I've never seen/heard of before.
Is this something that only happens in this scenario and only with the new unit models? If so, then there must be a problem with the graphic files extracting. They are located in part 2 of the mod folders. You might try manually extracting part 2 of the mod instead of having Civ 5 do it automatically. Here are the steps for doing so, as copied/pasted from the OP:
---If you need to manually extract the mods for whatever reason: Go to your MODS folder and locate the files that did not install in game. They will appear as civ5mod files, but are just storage files that can be extracted manually via a winzip type program. ie. the files that you downloaded off mediafire
For me it was
"WWII Full Earth Campaign Part 3 of 4 (v 3)"
&
"WWII Full Earth Campaign Part 4 of 4 (v 3)"
(Keep in mind parts 3/4 were removed, so in your case this would be "part 2 of 2")
Create a folder for each file and name them whatever you want (I just copied and pasted the above names and used those). Open them with your zip program and extract the contents to the corresponding folders you just made.
Now you've manually installed the mod files.
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Another potential cause if that doesn't work is that the new unit graphics are not working correctly with your video drivers. A simple fix for that is to update them. That's just a shot in the dark/blame the black box fix, as I can't think of anything else.