There are many techniques used to debug the working of vendor supplied msi file when one is developing a transform for the same. However I make use of a simple technique that involves the use of the verbose log file one generates using the /l*v command.
While analyzing a MSI for installation, repair or removal, generate a verbose log. For instance say we target a small area of the installation for analysis. Insert a small msg box using a simple vbs script at the junction. The moment the msg box pops up, open the log file and edit it using a distinguished marking like say '--' making a long line. You may also use '*' or '#' etc. The log file will need to be saved, i.e. save it with the same name at the same location. Resume the installation and now you will not have to read the entire log file but only a portion of it. I think this can be very useful for the beginners.
One can make use of more than one pop ups, like I generally use two to target a small area of the installation. All the activites done by the installer in that particular window is captured and highlighted in the log file.