Sorry, I can't find any information about using a custom server with Sync. Try this forum for help with Sync issues - Weave is the original name for Firefox Sync. http://groups.google.com/group/mozilla-labs-weave/topics

http://phaseshiftllc.com/archives/200.../setting-up-a-custom-weave-0-5-server has detailed description on setting up a custom sync server.

You're kidding. You have to go through that rigamarole just to put your bookmarks on your own server? Where's the simple FTP option?

Also, the above-linked article has a broken link. The link to the weaveserver (which is what you have to set up on your own server) is no good, and there is no obvious replacement. There are plenty of Weave-related repositories here:

http://hg.mozilla.org/labs

but it's not clear what you need.