We have developed a system that uses a single code base, consisting of four Visual Studio projects with an admin website, and customer facing website (each system has its own MS
You say you have one SVN repo with the code base for all the sites. So unless I'm misunderstanding, can't you simply move any shared components into that repository?
Things such as the in-page Javascript you mention should be made external where possible. If the HTML layouts are completely different, chances are the Javascript may be significantly different.
So this page in Site 1 and Site 2 is the same, but in Site 3 it does something extra which no other site requires or needs. We dont want this bespoke feature to be an overload as we dont want/need it for the other websites
Can't you extend the download code on site 3, so you have a common base across all sites, but extend it on site 3.