I would prefer the first approach: Just create my own project with my own stuff, and then drop that into my mojoPortal install. But, being pragmatic about the whole thing, maybe that is an exercise left for a better day and perhaps I'm better off following your suggestion. I'm mostly just at the playing stage right now anyway, so it's not the end of the work if something gets whacked.
Thanks for the effort of putting this together BTW. I was originally looking at DotNetNuke, which I'd used before on a previous job. However it seems to be very much SQL Server orientated, and I wanted to use MySQL instead. Nice to have an alternative.