Alright, messed with it enough. Figured out what I needed to do to get cleaner lineart scans:

1. Greyscale scan at 600 dpi (because scanner doesn't support 1200), save as .tiff
2. Mess with Levels setting until paper grain is gone (because I use rough paper)
3. Threshold, then index (1-bit)

Yay, learning by experimentation.