Thanks again.

Kyle
So the answer is in step 3, %APP_DATA%\Microsoft\FSX\dll.xml. You should create that folder structure and put the dll.xml file there, then run the installer and it will find it and modify it.1. Create this path in the registry: HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Microsoft Games\Flight Simulator\10.0
2. Add a new String Value: SetupPath ,= c:\program files (x86)\.... (whatever the full path to P3D is, including the trailing slash)
3. Copy P3D's dll.xml file (or its equivalent) into %APP_DATA%\Microsoft\FSX\dll.xml
4. Run the installer and you should be good.
It's going to add entries to that dll.xml file.
5. When installer is done, copy the dll.xml back to the P3D location.