I lost all my save progress in the process, but I finally managed to fix all of the problems I've been having by completing the following steps.
No Windows Compatibility Mode used at any part of the process, other than Run as Administrator. XP service pack compatibility can cause problems apparently.
1: Install Black & White base game via Setup.exe with "Run as Administrator" to a custom location on the Desktop.
(Warning: If you change the install directory, the installer doesn't create a folder by default, so you should create a new folder just for this game)
2: Install Patch 1, Patch 2, then Patch 3.
3: Download the p5dll.zip and extract p5dll.dll to the install directory.
4: Download and install all addons with "Run as Administrator".
5: Download BaW_Patch_2.exe and extract it to the install directory. Run it as Administrator and type fix for all commands.
6: Install the Fanpatch 1.4 (or higher if a new one's out when you read this) with Run as Administrator option.
7: Right Click runblack.exe, and under the Compatibility tab, check Run this program as an administrator and nothing else.
8: If you make a shortcut and it crashes or doesn't launch properly despite pointing to runblack.exe in administrator mode, try right clicking the shortcut, then under the Shortcut tab click Advanced, and check Run as Administrator.
And that should do it, it took me all of those ridiculous steps to restore basic functionality that I had when the game was new, but it looks great and runs great with the fan patch and it was worth the hassle.