Here's my two cents.
1. Don't worry about assigning numbers for S&E or method books. I'd just use a filing cabinet, in my opinion, with hanging files.
2. My categories are as follows. I start with 100 in each category. IE A100, B100, etc
A - UIL PML Pieces
B - Non-UIL Concert pieces
C - Concert-sized marches
D - Quick-step sized marches (We have enough that we separated, Military marching school here)
E - Christmas tunes
F - "Pop" tunes
G - Beginner tunes
For the JH music library we prefaced all of those same categories with "J". So JA, JB, etc. That helped us recognize "out of place" music.
Also, learn to use mail merge from an excel spreadsheet. It will help you make labels.
3. Buy a label printer. When you buy a new piece of music, assign the number and label it immediately. Buy a label printer (I use Dymo) and get it printed ASAP. As much as my OCD gets irritated by not everything being in alphabetical order, we just add new pieces to the end of the numbering system.
4. Get some help. Offer kids some pizza or something like that to spend a few days with you cleaning up the library. There are a few kids who will actually enjoy this.
5. Don't try to do it all at once. It will overwhelm you.
6. As previously stated, avoid filing cabinets. Shelves are better.
7. Make a master list of all pieces and the numbers that you can access quickly.