Hello Jacqueline,
Being able to open your PDF documents in iBooks is definitely an important feature, and thank you for all that information you provided.
The first thing I would try is resetting your iPad using the following steps:
Press and hold the Sleep/Wake button and the Home button together for at least ten seconds, until the Apple logo appears.
You can find the full article here:
iPhone, iPad, iPod touch: Turning off and on (restarting) and resetting
http://support.apple.com/kb/HT1430
If you still do not have an option to save to iBooks after the reset, you might try backing up and restoring your iPhone (you can restore the backup after restoring the iOS software through iTunes). You can find the steps to do that in the following articles:
iOS: How to back up
http://support.apple.com/kb/HT1766
iTunes: Restoring iOS software
http://support.apple.com/kb/HT1414
I hope this gets you back on track, Jacqueline!
Best,
Sheila M.