For this reason I need links refering to the existing site to be
relative.
Has anyone got any suggestions as to the changes I would need to make
in >the Wiki source?
I think a first suggestion would be to write an extension that takes <siteLink href="../myOldSite/page.html">Link</siteLink> and returns <a href="../myOldSite/page.html">Link</a>
Or really if your users are that savvy then just write out a link surrounded by <nowiki> tags. (i.e. <nowiki><a href="../link">Link</a></nowiki> )
-Courtney