How do I email a PDF I have saved on iBooks? I can't seem to do it since the latest upgrade.

It will depend upon whether the PDF allows it, some are protected and won't get the email option via the 'share' icon, you will only get 'print'. If you don't get the email option then you will need to connect the iPad to your computer's iTunes and do File > Devices > Transfer Purchases to copy it over (that will copy PDFs and epubs in the iBooks app, not just actual ibooks) and you can then email it from your computer.