In 2012, NARA announced a digitization project for Confederate records.

Thus far they have digitized several hundred volumes of Record Group 109 available for downloading, or on line viewing.

However, their five year schedule is overly ambitious, in my oinion.

http://blogs.archives.gov/TextMessage/2012/06/20/select-confederate-records-digitization-project/
Select Confederate Records Digitization Project