I know that you have uploaded a good many high-quality color scans of engraved scores so I'm going to assume you are talking about reducing the file sizes of those pdfs. To the best of my knowledge any attempt to reduce the file size of a pdf that consists of color images will result in a loss of quality if you want to keep the images as full color. The best option, especially since you are working with engraved scores, is to reduce the color palette to black and white (2 colors) and have Acrobat pack them using CCITT level 4 compression. For a 600dpi image of a piece of sheet music that will usually reduce the file size for an individual page down to less than 150kb.
Are you scanning individual pages as individual color tif files or does your scanner directly output the files into a color pdf? My place of work has network copiers that do that. If you are producing color tif files then you might want to try running them through Scantailor. This application has the ability to de-skew, crop, set margins, and convert images to black and white. The output files can then be packed into a pdf by Acrobat using CCITT level 4 compression. Geniusboy98 has written a nice tutorial for using ScanTailor. If your scanning method creates the pdf directly then you can use Acrobat to export the images out as color tif files (probably using either no compression or LZW compression--you wouldn't want to use a lossy format like jpg). Then, run those images through ScanTailor.
I use a combination of Imagemagick and ScanTailor. For me, Imagemagick handles the re-sampling to 600dpi (since most of the images I deal with are taken from the web they tend to be anywhere from 120dpi to 400dpi) and the conversion to black and white tif files. I then run those images though ScanTailor in order to de-skew, crop, and set uniform margins. I can give you the scripts to use with Imagemagick but you might want to try running your raw images through ScanTailor first and see if the output is satisfactory on its own.
generally, scans / images in color or grey scale are rather large, of course. When I convert scores I generate bitmap, so the file size of the .tif is much smaller.
My procedure is as follows:
I check if there's already a set of filters available... (meanwhile I have created many different batch commands for dark scans, yellowish scans, low resolution scans, dark grey scale, etc....) Otherwise I try with different settings and different filter until I get the best result (with best possible resolution)
In order to upload a file to the USA server, you need to be on the Classic Skin for the website (click on the "Switch back to classic skin" link at the bottom of any page if you are on the Modern skin currently), then go to "Add File" (upper right hand corner under search bar), then click on the tab you wish to upload the file under. On the Add Files page find this: "If a file is public domain only in the United States (e.g. was published before 1926 but author died less than 50 years ago), [more...]". Click on "more..." to reveal a link to click on "this upload form", click on this. This takes you to the PML-US Server page, from there upload a file here under "File upload". After upload, this redirects you back to "Add Files" page previously, and fill out the rest of the info on the page as normal.