1) Disable all your custom software delivery tasks and patch managment policies.
2) Export the various trees - Software Delivery task, Patch Management Task (probably optional for both if you don't intend to recreate them). The clients will always be looking for any active tasks\packages assigned to them. So if they were disabled before you rebuilt, that's a big step. However, if you're going to use the same policies and tasks again, it will save you a ton of time.
3) Export the Software Delivery packages and (optional) Patch Management packages.
4) Export any custom reports and collections (be sure not to use the same names as your tasks or packages export - they will overwrite if you're not careful).
5) Note any specific settings you have set - purging, check in times, bandwidth throttling, etc.
Keep in mind that, due to a Microsoft limitation, that .xml files, can only be of a certain size when you import them, or it gets rejected. So, break the exports down, just as you have them listed in the console (pilot, test, business group, etc).
I'm sure there's more, but you've got a bit of tough task ahead. We will be happy to help.