OK, it seems that I am making some progress, thanks for the help. Here's what's happening:
I created a new setup.exe that applies the transform to the MSI. When I click through the wizard, accepting the defaults that I have setup, the install runs properly. When I use setup /s /v"/qn", the setup runs silently and installs some files, (it appears to be common files, .dlls, etc.), but no executables or shortcuts. Have you ever seen this before?