Thanks to the forums at the Company of Military Historians, there are a couple websites made known that provide online access to Civil War manuscripts. The first is Manuscripts of the Civil War: Diaries & Journals, which is affiliated with Notre Dame. The other site is called Civil War Manuscripts Project, which is part of the Connecticut Historical Society. If you are interested in researching, or simply reading Civil War manuscripts, then check these sites out.
Civil War History
The Blog Between the States.
The two websites linked seem to be down.
The Notre Dame one is up, but you are right, the other one is down, albeit temporarily, I believe.