Interesting and good work! I'll admit to only reading the last few pages and looking at the results, but I'll still throw in a few comments. Overall, I think this looks very nice. I am a bit iffy on the use of a single letter to designate a double vowel. That's coming from me as a native Finnish speaker, btw.
If AA, EE, UU, YY and OO are single letters, so should AI, EI, UI, OI, AE, OE, UE, AU, EU, OU, etc. They're pretty much the same concept and having one designated by double letters and not the other does not seem logical at all. It would also be a very distinctive element in the language, separating it from the more typical (to most of us) Latin based letter sets.
One particular letter or pair of letters needs to be separately addressed as well, in regards to pronunciation. That's Y and J. The Japanese "Ayo" is pretty much unpronounceable in the Finnish way (well, not unpronounceable but it sounds very funny/ugly). Y is after all always a vowel sound in Finnish, so the way to write the Japanse pronunciation out in a Finnish way is to use "Ajo". My gut instinct is to say that the Caldari Y (and J) is in all cases similar to the Finnish one (it fits the words and pronounciations I've seen). Hence, btw, the english "yo" would be written as "jou" in Caldari. However, as above, I suggest that should only consist of two actual Caldari letters (since OU should be a single letter).
Just a few thoughts.