Ok, I did a test tonight and scaled all the ships to each other, keeping the TOS Connie at a length of 22 inches. This resulted in the D being WAY too big for the case, so I had to scale all of them down by roughly 23% in order to have the D fit comfortably. Here are the results:

While it doesn't look
terrible, I don't prefer this because a) it breaks too far from the canon apperance, and b) it makes the display very right-heavy and thus light and sparse on the left side.
Having satisfied my curiosity, and having a better idea of how the ships relate to each other, I then went back to my original configuration and took what most of you recommended into account and sized the C and D up a bit, and the E down just a smidge. Here is my new "idealized" result:

I like these proportions a bit better, but if I were to do anything it would be to scale the E back up to where I had it, because now it looks too small, even though that's roughly it's size compared to the D. EDIT: I think I'm going to add a tiny plaque somewhere inconspicuous that reads: MODELS NOT TO SCALE
Here is the canon appearance, just for ease of comparison:
Thoughts?