Tuberculosis (TB): Given the patient's prolonged fever, cervical lymphadenopathy, elevated CRP, and presence of small lesions in the liver and spleen suggestive of granulomas or small abscesses, TB is a strong consideration, especially in a region like India where TB is endemic.

Brucellosis: This zoonotic infection can cause prolonged fever, lymphadenopathy, and involvement of the liver and spleen. It's a consideration given the patient's symptoms and the presence of lesions in the liver and spleen.
Typhoid Fever: Although the CT thorax and CECT abdomen findings might not be typical, typhoid can cause prolonged fever, and in some cases, liver and spleen involvement. The diagnosis should be considered, especially in areas where typhoid is common.
Lymphoma: Given the lymphadenopathy and systemic symptoms like fever, lymphoma could be a consideration, although the presence of liver and spleen lesions could also suggest other diagnoses.

Malaria: Although the patient has been febrile for 21 days, which is longer than the typical cycle for most forms of malaria, certain types like Plasmodium vivax can cause prolonged illness. Given the potential for severe outcomes if untreated, malaria should be ruled out, especially in endemic areas.
Endocarditis: Infective endocarditis can present with prolonged fever, embolic phenomena, and multi-organ involvement. Although less likely given the absence of heart-related symptoms, it's a diagnosis that could be deadly if missed.
HIV/AIDS: Given the patient's prolonged fever and multi-organ involvement, an HIV test should be considered, as HIV can predispose to a variety of opportunistic infections and malignancies.

Histoplasmosis: This fungal infection can cause prolonged fever, lymphadenopathy, and liver/spleen involvement, especially in immunocompromised individuals. It's less common in India but could be considered in the differential diagnosis.
Cysticercosis: Caused by the pork tapeworm (Taenia solium), cysticercosis can lead to a variety of symptoms depending on the organs involved. While less likely, it could be a consideration given the liver and spleen lesions.
Sarcoidosis: Although rare, sarcoidosis can cause granulomatous inflammation in various organs, including the liver and spleen, and could be considered in the differential diagnosis, especially if other causes are ruled out.