According to the National Park Service, the answer is: THREE
F. A. Rasch, Phillip Prosser, and R. E. Cook
"Of course, all the Confederates buried in the trenches are unknown, having been buried as a mass by the enemy who did not know their identity. Only three Confederates now lie in the Shiloh National Cemetery: F.A. Rasch of the Orleans Guard (who is in an unknown grave), Phillip Prosser of the 13th Louisiana, and R.E. Cook of the 18th Alabama. Work is continually ongoing to compile an accurate list of Confederate casualties." NPS Link
1) F. A. Rasch of the New Orleans Guard
2) Richard E. Cook of Alabama who according to Fold 3 was a member of the 18th Alabama wounded in the head at 11 am April 6th, and captured at Shiloh
3) Corporal Philip Prosser
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