ITNinja

Microsoft has provided their Office Custmization Tool (OCT) to customize and package Microsoft products like MS Access and likes.

Refer This link :

http://technet.microsoft.com/en-us/library/ee656738.aspx

to understanf what OCT is and how it works.

Also refer this link:

http://www.itninja.com/software/microsoft/office-visio-professional/12-782

This approach is the preffered way to customize MS products  and much convienient too.

You don't want to repackage Visio since it's already based on MSI. Repackaging a MSI is bad practice, you should never do that.

As akki said, use OCT. You can start it by running setup.exe /admin