Ken,
Thank you for the suggestions!
We are going to use custom built climate controlled cases similar to what you what find at the NBTHK in Tokyo. Space is our enemy right now. With the sqft we will be working with we have to be very selective. For the soft open we will likely display around 30 swords, 5-10 armor, 5-10 yari & naginata, and many other items.
The rooms will be broken down by era, but I may need the help of the board to ensure the groupings are proper.
I am sorry you had those issues with your university. This is a self funded project for now, but we have interest from other parties for support. We will see what flushes out. I believe my university may back it if I can built out a large enough section to cover the rise of Christianity in Japan. On that note, it has been very difficult to locate reasonably priced (crypto-Christian) items that touch on this subject.
In any event, I'm really glad I have people such as yourself, and other members of the board, willing to share their thoughts and experiences. It will help tremendously.