I am upgrading my IPad to 9.3 via windows pc. I have transferred purchased items to Itunes. It still indicates there are items to transfer---I presume these are items not purchased via the Itunes Store. If I upgrade to 9.3 will I lose them?

Upgrading to 9.3 should not result in any loss. However, I recommend backing up your iPad, importing the pictures, and copying important data. While most updates go smoothly, some occasionally do not.

Regardless, I don't know if you are aware of the bugs with iOS 9.3. Many or most have updated without problems but many have had serious issues. This thread and article provide details. If I were you I would wait to update until the next fix is issued.

For those having problems with the iOS 9.3 update please read...

http://osxdaily.com/2016/03/25/troubleshooting-ios-9-3-update-problems/