If you made the changes to CMC/ Infoview properties files in custom folder, repair will not overwrite the changes made in custom folder. Take backup of any files you made prior to upgrade.
Applying the patch on top of SP4, should be strightforward as long as you follow best practices. Is your environment clustered?
If it is single server, make sure SIA (Except CMS) and Tomcat is stopped. Run the patch installer.
If it is clustered, run upgrade patch on CMS servers first , and then on other servers.
if you still not comfortable doing by yourself, as Henry suggested contact Support.
