Just and update, I found a linux utility to read raw data from the floppy drive. It seems I can get more data off the floppy this way without running into read errors. If I get an image written, how do I store the track info in the image file (ie: for use with dosbox)?
The floppy I'm reading is DSDD so it was two sides (two heads). Not sure if I store each track of data and alternate each side (track-0-side-0, track-0-side-1, track-1-side-0, track-1-side-1) or if I write all of side 1 to the image file, and then append all of side 2?
Link to the utility for anyone interested:
http://www.fdutils.linux.lu/index.htmll