Here are the changes we make to the installed instance of trac that I can remember:

• our main.py in trac/web is different (beaversource:/usr/share/python-support/trac/trac/web$sudo cp ~/bs_admin/trac-0.10.3/trac/web/main.py . )
• as well as our chrome.py in trac/web is different (beaversource:/usr/share/python-support/trac/trac/web$sudo cp ~/bs_admin/trac-0.10.3/trac/web/chrome.py . )
• our index.cs template is different (apache has the config PythonOption? TracEnvIndexTemplate? /data/trac_index.cs, this is unaffected by upgrades to trac)
• we use a different set of templates to makes usernames into links to elgg profiles (beaversource:/usr/share/trac/templates$sudo cp ~/bs_admin/trac-0.10.3/templates/* . )
• we globalize the beaversource theme (beaversource:/usr/share/trac/htdocs$sudo cp -R ~/bs_admin/trac-0.10.3/htdocs/* .)

This is all I recall for now, but it does seem to do the trick.