Would like to be able to see and click the reference verses that show in the middle of the printed bible.
By "references" do you mean cross-references? If so, did you read this existing thread here: http://www.equipd.me/forums/threads/no-cross-references.20/ Please let me know if that answers your question or not...
Yes cross-references. If they are not included in the EPUB then maybe allow us (the users) to enter or do the cross-references manually? Examples clicking on a word or a verse that allows us to link to another bible verse on the bible.
I think this is a very good idea. The implementation could be somehow similar to Strong's words. Inside the popup you can click on other references such as Word Origin and navigate to the definition with the ability to navigate back. I am sure is not an easy implementation but could prove a very powerful feature.