If I were approaching this, I would do the following:
- Create a branch or whatever variation on a branch your VCS supports for the change.
- Swap in jQuery 1.4 for jQuery 1.3
- Test extensively to see what breaks - if you have any automated tests, this will be so much
the easier
- Depending on what breaks in the legacy packages, see if you can fix it (assuming all plug-ins are open source) or if there is a suitable under-development replacement that supports 1.4
- If any of the plugins are still under development, take this opportunity to upgrade to the latest version (both for 1.4 support and because the latest version likely fixes bugs, etc).
- If you can fix everything you need to fix, merge your changes into the trunk and call your upgrade a success.
Of course, depending on the size and complexity of your code base, this could be a more or less expensive procedure.
EDIT: combined with jvenema's excellent point, you have a nearly fail-safe way to make sure you get to the success point. If something breaks, just throw in the plug-in.