I rarely scan music; but when I do I tend to find that using a monochrome scan with a threshhold is either really good or really bad.

Usually I scan in full colour and (if possible with the scanner) adjust the exposure settings to reduce bleed-through from the music on the back, as the paper can be really thin. I then reduce down to a suitable colour depth using Photoshop.

In terms of resolution I don't find theres much to be gained by going past 300 dpi. On older scanners they get higher resolution using software interpolation anyhow so you don't gain anything in real terms!

What can sometimes help to clean up rough edges is to use Photoshop or similar to resample the scan to a much higher resolution then apply smoothing and resample back down again. Overdoing this can reduce clarity, however.