The Definition of the Leed Boundary - How can I be sure that I have made the right decision?

You can ask GBCI for a conference call or to take a look at your proposed boundary via email. No need for a CIR. The reviewer would rather not deal with major boundary changes either! You should get a LEED Coach contact when you register the project, and you can email that person, describe why you have doubts about where to draw the boundary, and ask to discuss before you move forward with documenting the project. I'd suggest marking up a site plan with the different proposed boundaries so it is clear what they affect. 

I'd suggest sending a question by email requesting a conference call, so that you can review the proposed boundaries with GBCI staff. The more detail the better so they can assign the right person and have an answer prepared before the call. I wish I had an answer for how to speed up a response, it's been taking a few weeks on my registered projects recently too. You're not doing anything wrong, they're just dealing with a ton of questions right now!