Bardfilm, that does seem like an awful lot of faffing on! Have you considered simply doing it the way I suggested earlier? In iTunes, select a book in a series and rename the title by giving it a a common prefix and number. For example
Harry Potter and the Philosophers Stone becomes HP1 - Harry Potter and the Philosophers Stone,
Harry Potter and the Prizoner of Azkaban becomes HP2 - Harry Potter and the Prizoner of Azkaban
iBooks definitely then stores them in the correct order. I suppose if you wanted them to PLAY concurrently you could make them 1/34, 2/34 etc (the HP books break down into LOTs of parts!). Whereas in the old Music app you could put all the separate books in a series in a playlists to get them to play concurrently. I haven't tried that with iBooks just yet as sadly my iphone has just broken, but it might be worth checking out.
I have also used the "sorting" option similarly within iTunes. So the Harry Potters are just HP1, HP2, HP3 etc, but the I also have a sorting category for autobiographies, biographies too so that within that category they are alphabetical, but at least I don't have to remember what someone's autobiography is called to find it, I know they'll all stack at the top of the book list.
It is a bit tedious coming up with a prefix for books, but sometimes I use the name of the main character eg Dresden 1, Dresden 2; or I abbreviate a common part of the title eg Ladies of Letters go......" becomes LOL1 - Ladies of Letters go..."
What I HAVE enjoyed about the iBooks app is that you can see the chapters again, which you used to be able to do in the Music app, but then they stopped! It makes moving around the book easier than tilting your finger to move along the scrubber, to move backwards and forwards more than 15 seconds!
Overall, I'm now over my complaints of the iBooks, except that it still peeves that they are separate apps, but the functionality I can use in the iBooks IS better than listening to audiobooks in the old Music app imho
Rowena