Hi,
The piano roll project sounds fascinating, and there are a number of folks who are working to scan and save these.
You may find the ReBar feature to be more helpful for your purposes. It will help you to correctly line up the barlines where they belong, and should also help with cleaning up the alignment issues you mentioned as well.
You'll find a short Tutorial Video to get you started at
http://www.notation.com/vb-forum/showthread.php?t=4064
and detailed step-by-step instructions in Help/Users Guide - just use the Index to look up "rebar".
Enjoy!
Sherry