Unfortunately the answer is no. We originally had our source code in an svn (Subversion) repository at Novell Forge, but they closed down and we moved to hg (Mercurial) at Codeplex in May 2010. So I don't know of any way to get the code as it was at version 188.8.131.52.
The biggest concern from what you mentioned though is that it was customized, if by that you mean they forked the mojoPortal code by modifying it then even if you could get the original code it would not have the customizations. I always tell people not to fork the code, doing that usually ends up coming back to bite someone in the long run. If they did fork the code they should have kept a copy of it.
It all depends on what is meant by customization, if it was just custom skinning, it should be possible to upgrade but I would do a practice run on a copy and work through any issues such as needed changes to fix older skins before attempting it on a production copy. Note also that we no longer support SQL 2000 so if they are using that it would be problematic to upgrade, SQL 2005 and up is fine.
It is also possible to implement and plugin custom features without forking the code but if they did that I would still expect them to have source code around.
Wish I could give you better news, I don't envy you having to figure out whether they forked it or not and trying to find a path forward if they did fork it and no longer have the code.