I think the subject says it all. The original game included two spellbooks (wizard and cleric), and GOG is only providing the former. I found the latter here: http://www.roms4droid.com/manuals/.download.php?name=Ultima%20III%20-%20Cleric%20Spellbook.pdf&reldir=PC%20Games/Misc/

(it's a weird-looking page, but the download works.)

The Player Reference Card (which lists all the keyboard commands -- the manual only specifies a few) is also missing. Found one for the C64 version here; most keys seem to be the same: http://www.digitpress.com/library/manuals/c64/index.html

I got my cleric spellbook from replacementdocs, they have tons of manuals which is really hand for older games where the interface is not sel-explanatory. Strategy Wiki also lists a lot of ressources for getting started and everything else one might need:
[url=http://strategywiki.org/wiki/Ultima_III:_Exodus]http://strategywiki.org/wiki/Ultima_III:_Exodus[/url]

Yeah, the included documentation for the Ultima games sucks, some of it is incomplete and the DPFs are not well scanned.