After some back and forth I've managed to fix Single Sign On for the Wiki. There is one problem I've encountered tough, if you log out of Joomla you're still logged in, in the Wiki.
I don't think it's a security issue, just a fluke. I've been reading a bit about JFusion and DokuWiki. Seems the JFusion devs are/where a bit frustrated with frequent changes to the authentication code in the wiki.
I'll keep an eye out for a solution, but I regard this as minor.