You can copy your purchases to your computer's iTunes via File > Devices > Transfer Purchases - that will also copy PDFs and epubs that are in the iBooks app. You can then sync them to your other iPad.
If you want everything from your old iPad on your new one, then after doing Transfer Purchases back up your old iPad (File > Devices > Back Up) and then restore that backup onto your new iPad (that will replace the current contents of your new iPad with the backup).
Transfer content to a new device : http://support.apple.com/kb/HT2109
Using iCloud to backup and restore may not copy all of your purchases onto the new device, not all purchases are redownloadable - using your computer's iTunes, and doing Transfer Purchases, should copy them all over.