John, I did a very small sampling of fifty Confederate deaths in alphabetical surname order. This by no way includes all the various death reasons. The following is what I found.
Death due to pneumonia = 20
1 = Nov - 64
2 = Jan - 65
9 = Feb - 65
6 = Mar - 65
1 = Jun - 65
1 = Jul - 65
Death due to small-pox = 11
2 = Sep - 64
1 = Nov - 64
2 = Dec - 64
3 = Jan - 65
2 = Feb - 65
1 = Apr - 65
Death due to typhoid fever = 5
1 = Jul - 63
1 = Jan - 64
1 = Sep - 64
1 = Oct - 64
1 = Jan - 65
Death due to diarrhea = 4
1 = Aug - 64
2 = Jan - 65
1 = Mar - 65
Death due to debility = 2
1 = Feb - 65
1 = May = 65
Death due to jaundice = 1
1 = Sep - 64
Death due to dysentery = 1
1 = Oct - 64
Death due to intermittent fever = 1
1 = Mar - 65
Death reasons unknown = 5
4 died in 1862
1 died in 1863
Total deaths in 1862 = 4
Total deaths in 1863 = 2
Total deaths in 1864 = 12
Total deaths in 1865 = 32