The MHS has a collection of paintings of all the Civil War flags held by the state in the 1890s. These were done by John Weide. The page with the 35th Mississippi flag is:

http://collections.mnhs.org/visualresources/details.cfm?imageid=141967&Page=1&Keywords=weide&SearchType=Basic

The 39th Mississippi Flag remnant can be seen at:

http://collections.mnhs.org/visualresources/details.cfm?imageid=141972&ImageNum=5&Page=1&Keywords=weide&SearchType=Basic

The small scraps can be seen at:

http://collections.mnhs.org/cms/display.php?keywords=mississippi+flag&irn=10243082

Now here is something to think about. Only the flag of the 35th Mississippi is depicted as having any battle honours. If you compare the remains of lettering on the one red scrap it does not match with any of the battle honours visible on the 35th's painting. The one letter looks to be an "S", but it reversed. If this was a painted letter it would fall to reason that the letters on one side of the flag would be reversed, but here the letter is appliqued. So why would it be reversed?

Ryan