Trilogy trouble

I'm working my way through the second riddle quest book this week.  I have 65,000 words of a very old rough draft to work from.  I want all three books to be riddle quests, and the first book I've already written, and worked out all the clues for.  I have added some tweaks to my original very old story, but the basic story remains the same.

The second book is a riddle quest based around old paintings.  They are the artworks of a long-vanished alien civilisation, and depict various military scenes.  I originally had my characters finding the next clue from the name and geographical clues in each painting.  Now I've added a written riddle on the back of each work.  These will lead  to a downed alien ship and its files.  

So far, so good, but that only takes me to the end of book two, so what about book three?  I've said  in book one that the aliens were master bioengineers, and that they had a massive army of bioengineered soldiers.  Now I've decided that there are five of their bioengineering facilities still hidden on Vedrana.  They will be in remote areas, and will all be buried undergound.  That will explain why some nosy archaeologist hasn't already stumbled over their remains.  But now I have the problem of creating riddles for these last five sites.

And here I've tracked back into book two again.  I've hidden the clues for book three in the paintings which are clues for book two.  At the end of that quest, when they recover the ship's files, they contain references to the bioengineering sites, but the locations are alien names, which no Human now knows.

Arrien's soulship can decode the aliens' language, so she can find the aliens' names for the bioengineering sites they need to destroy.  Now all they have to do is work out the current names for those places.

Which is where the big cats I've added to the paintings for book two will come in.  There names are clues to the locations of the bioengineering sites.  Our heroes can now discover the human place names, and that will lead them to the hidden sites.  The alien ship's files will tell them what was manufactured at each place, and include  passwords.  So they can go in, shut down each site's defences, and then destroy them. 

Getting these three sets of clues right has been one of the most complex planning exercises I've ever undertaken, but I think I've finally got them right.  Now I need to go off and write the rest of book two.