My iPhone will not let me download my books that I purchased on my iPad. Says something about only one apple ID can be used on that device every 90 days.

Have you used another account on your phone for iTunes match, automatic downloads or re-downloading past purchases : http://support.apple.com/kb/HT4627 ? If you have then you will need to wait until the 90 days have completed before you can link it to another account - you could try copying the books from you iPad to your computer's iTunes via File > Transfer Purchases (File > Devices > Transfer Purchases on iTunes 11) and see if you can then sync them to your phone