I was just about to point this finding out.Did you notice the positive PCR test for MS? That usually stands for mycoplasma synoviae or MS, which is a respiratory disease that causes infection and swelling in the leg and foot joints.
Clostridium perfringens is a rod-shaped bacteria, and a common cause of necrotic enteritis. Necrotic enteritis frequently follows coccidiosis infection. The protozoan was probably an opportunistic illness in the already compromised immune system, due to coccidiosis and the NE.
Thank you for posting the necropsy results. It is always interesting to read the findings of the poultry vet, and helps us all learn.