Geoffrey Steadman is the guy for this. He's created a number of readers (secular Greek). See
http://geoffreysteadman.wordpress.com/. I've had some contact with him about creating a Reader's edition of Epictetus' Enchiridion. Geoffrey uses MS Word and no database. If you contact him, he would be more than happy (I believe) to give you some advice.
I have created an MS access database with many Greek functions that would be suitable as a base engine for working on a Reader's edition. The base format can be found at
http://www.letsreadgreek.org/resources/ under ntdatabase3.mdb. It needs some updating, but it is a frame for starting and has betacode/greek transformation tools. It would perhaps be useful to turn this database into a Reader Creation tool.
Those are my ideas. You need to create a base vocabulary -- what the frequency is for words in the back is what determines what vocabulary is listed on same page as the text. Then you need grammar notes for the difficult constructions. It's best to use a text from 1921 or earlier. That way you have no copyright infringements. A Reader's format is becoming a standard kind of thing; look at Deckert's Koine Greek Reader, Steadman's readers, The USB Greek Reader's NT and some of the other standard readers out there. If your book fits in - it works. You should also think about where you will publish your book - with Print-On-Demand available, there are a number of options. Lulu, among others comes to mind.