Hi. I'm also having trouble with this same issue. I have spent about 3 hours on it now and just don't understand the instructions that have been given in other posts.
My issues:
I copied "Beyond the Sword" folder from my user account folder into "C:\Games\Beyond the Sword\". After this, I installed BUG 4.3 using the second option mentioning AltRoot method in it.
Next I went and took a look at BUG Mod\cvaltroot.py. Basically I understand what this file is supposed to do, but I'm unsure what this file should look like after editing.
Mine was:
"C:\Games\Beyond the Sword\"
and nothing else.
I'm unsure what to do with the Rootdir part and what it should contain.
Also when trying to edit my shortcuts, the edits don't get accepted. I get an error how the path is wrong and so on. Which leads to my next question; am I supposed to edit the "Play Bug 4.3" shortcut OR "Civ4BeyondSword" shortcut?
Sorry again for this, but I managed to get BUG working on my work computer, which doesn't have any weird letters in the username, but my home computer does, so now I'm utterly lost and don't know how to live without BUG anymore.