I am a student developer and I have built several installers for the company I am working with now. So I am fairly familiar with WIX.
We recently decided to have a Build server
I had a similar situation where the source path of the files was to be passed as a command line argument to the build script. This is what I did:
Edited the wixproj file and added the following content under the "PropertyGroup" node:
R:
where R: is the default directory/path from where to pick the source.
Now, the source can also be passed as a command line argument during build: