Sorry but I cannot offer any support or advice for forked versions. I recommend don't modify any mojoPortal code and don't add code to the mojoPortal projects. Custom code should be in your own projects so they are compiled into your own dlls not in our dlls. Once you've gone down that path of forking the code or adding your own code to be compiled in with mojoPortal code you are on your own and if you decide to stay on that path you will have to figure out your own strategy for merging any updates from our repository.
Note that version numbers only coincide with database changes, ie the version number only changes when we need to run an upgrade script on the database. Lots of other changes and progress happens in the repository without any change to the version number.
For people who don't modify the code it is easy to update at any time from the repository, the steps are: pull changes, apply changes to working copy, rebuild solution, visit /Setup/Default.aspx in case there are any new scripts that need to run.
We have a whole series of training videos that shows the recommended way to develop a custom content feature that plugs into mojoPortal without modifying any mojoPortal code.