Answer

1. Download the Windows Installer 3.1 .exe file from Microsoft:
   
   http://www.microsoft.com/downloads/details.aspx?FamilyID=889482fc-5f56-4a38-b838-de776fd4138c&displaylang=en
   
2. Place the downloaded .exe into C:\Program Files\Wise for Windows Installer\Stub\3.1.
3. To have your .msi file pre-install this version, you must create a single file .exe file which will create an EXE wrapper. This option is located on the Build Options page in Installation Expert. Go to the Prerequisites page in Installation Expert, click Add > Prerequisite and browse to the Windows Installer .exe file. It should show up in the list of available prerequisites at this point.