I think maybe it's not entirely clear what you are trying to do. It's generally advised not to make any edits to mojoPortal code, but rather have a separate project where you write all your custom code. There are, however, a very few instances where I have inserted a custom line or edit to the core code. In those cases, I just keep them well documented in a file in my main custom project and restore my few customizations each time I update my mojoPortal code from Codeplex. If you need to make a minor edit to the global.asax file, you could do that and just keep the change documented somewhere outside of the mojoPortal code. If you need a custom HTTP Handler, I think that would be something altogether different.

John