I'm still looking for a better set of instructions, but this is what I have.
If you use different Apple ID's, then I recommend you create a new user on your computer and set up his iTunes library separate from you own using that log in. If you use the same Apple ID (so that you can share all your apps, music, etc) then setting them up in the same library is better, though it may take a while to smooth out the wrinkles.
Apps and iBooks can always be downloaded again, for free. A hassle, but not a big deal. However the content of those apps can and will be lost without care. I recommend making backups of those files (separate form iTunes) if possible.
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Here is Apple's recommendations on how to transfer all your stuff to a new iPhone. With a few modifications it works very well for moving your iPad to a new computer. Wish I could find one as well written for the actual task.
iOS: How to back up your data and set up as a new device
Start by going into iTunes Preferences (before connecting the iPad) and turning off auto-sync. It is under the Devices tab. This will prevent any unwanted syncing before you are ready.
Do only the parts that apply to your information/situation (i.e.; if you are syncing contacts with Google, don't do the Personal Information Manager part. Stop when you get to the Restore step.
It would be wise, after the Transfer Purchases option to go through iTunes and make sure everything (media, app, book) got transferred. If not you may have a few more steps to insure all your stuff gets safely backed up on the computer.
NOTE: If you have picture albums in the Photos app, and they are not backed up somewhere other than the iPad, you need to save them first before doing anything else. The first sync will remove them. The PhotoSync app works well for this, and you can use it before starting any of the other procedures.
The quality of the pictures recovered this way will probably not match the originals. iTunes optimizes photos for viewing on the iPad when it syncs them.
