Disabling auto update can be done with an setup argument. Please read this topic http://en.pdf24.org/forum/about874.html. There you can find all supported MSI setup arguments.
Currently I can't assist you in editing the MSI. This is not quite easy. You have to do it yourself.
Maybe we will add a new command line argument too load an alternative logo, but this is currently not supported.
It would be easier, if you use the current msi setup. Run the Setup with AUTOUPDATE=No
After installation copy a logo.bmp file to the install directory to change the default logo.
This is I think easier than changing the MSI file.
A small script could do the job.