Back up the PC up first. Then you will be able to reinstall the data drive, or those portions that you need/want.
Anything synced with the iPad will stay there, unless you try to sync it with the empty iTunes library later. Here are some instructions that may help, when it comes time to connect the iPad back to the computer.
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.
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.
