I am not authoritative here, but with past experience I can shed some light.
How should the scan quality be? What DPI, use anti-alias/blur or not, other scanning options?
300dpi is considered ideal. Lens/glass refraction and blurry edges are apparent when smaller DPI is used, scratches and dust when larger without clarifying the image other than magnifying its inkjet spray pattern or dye sublimation diffusion.
What image format should I save the pages as, before compiling them into a PDF?
24bit BMP/TIFF/PNG/TGA. Do not save to lossy formats (JPG, 8bit/indexed PNG, GIF, PPM, PCX).
How should I crop the pages? If a page is scanned straight, but the print on it is slightly slanted, should I adjust it and crop away some of the empty page?
Starting at the actual upper left of the paper, crop to the exact dimensions of the paper, consistently through all the magazine pages. This is often 8 3/8” x 10 7/8” for US publications, but identify the standard of what you are scanning.
Pages should be scanned at a consistent angle, as close to straight as manageable by your equipment. This often means sacrificing the binding to avoid curves and shadows. You may use Scan Tailor
if you really need to make adjustments to your scans, but such software corrections will blur and distort the image to a certain extent, so it is best to avoid the step entirely.
Can we add our username as the author/scanner information in the PDF?
This metadata is generally stripped during the baking process prior to datting, so it would be meaningless to write anything in.