Software Deployment Question
Packaging Access Runtime 2013
Community Chosen Answer
It does get a bit upset if you edit the MSI.
As noted above, do your modifications in an MSP by running setup.exe /admin.
Most of what you want to do can be done from the Config.xml. Reg keys are a bit different, add them using the /admin (they will be in the MSP) but they don't get un installed.
Most places add (and remove) reg keys using a script in the config.xml (create a 2nd XML for removal)