Ok, first, regarding the facing pages, yes, this is a problem when adding/deleting pages. If the margins are the same for left and right it is not a big problem, but when the margins are different, such as having a larger inside margin, you get this mess!
I could offer suggestions if I could see the document, but not knowing the complexity of it, I cannot.
Maybe you are better off doing a single page document for this. You can still make separate right and left master pages. Of course if you add or delete pages, you might need to reverse some items. Again it is hard to tell what you are dealing with.
Regarding the blank pages being printed. Two thoughts. One, is your entire document linked? I would look through the entire document. Easily done in say 50% view and watch the links and see where they go. Are the blank pages linked as well? It seems not all blanks are printing, as you say most show up in the middle.
If it is sporatic, could it be your printer is picking up multiple pages due to the paper? Too dry?
I'm sorry I cannot help more. I would need to see the document.