Fibromyalgia: This condition is characterized by widespread musculoskeletal pain, fatigue, and tender points, which could explain the deep bone ache. The need to constantly crack joints might be related to the patient's attempt to relieve tension or discomfort, a common behavior in individuals with fibromyalgia. The onset of these symptoms a couple of months into the long Covid healing journey could be related to the post-viral syndrome often seen in long Covid patients.

Hypermobility Syndrome: This condition involves joints that move beyond the normal range, which could lead to the need to crack joints frequently. It might also contribute to the deep bone ache due to the instability and potential for microtrauma in the joints.
Osteoarthritis: Although less common in younger individuals, osteoarthritis could be a consideration, especially if there's a history of joint trauma or repetitive strain. The deep bone ache and the urge to crack joints could be symptoms of early osteoarthritis.
Vitamin D Deficiency: Vitamin D deficiency can cause bone pain and muscle weakness, which might be exacerbated in the context of long Covid recovery. The deficiency could contribute to the deep bone ache and potentially to the joint cracking behavior as a way to relieve discomfort.

Multiple Myeloma: Although rare, multiple myeloma is a type of blood cancer that can cause bone pain, which might be described as a deep ache. It's crucial to rule out this condition due to its severe implications and the need for prompt treatment.
Osteonecrosis: This condition involves the death of bone tissue due to a lack of blood supply and can cause severe bone pain. It might be a consideration, especially if the patient has been on long-term corticosteroids for Covid-19 treatment or has other risk factors.
Lymphoma: Some types of lymphoma can cause bone pain and might be considered in the differential diagnosis, especially if there are other systemic symptoms such as fever, night sweats, or weight loss.

Ehlers-Danlos Syndrome: A group of disorders that affect connective tissues supporting the skin, bones, blood vessels, and many other organs and tissues. While rare, it could explain the hypermobility and potentially the bone ache if the patient has an undiagnosed form of this syndrome.
Sickle Cell Disease: In patients with sickle cell disease, vaso-occlusive crises can cause bone pain. Although less likely, it's a consideration if the patient has not been previously diagnosed with this condition and presents with other suggestive symptoms.
Hypothyroidism: Severe hypothyroidism can cause musculoskeletal symptoms, including bone pain and joint stiffness. While not directly related to joint cracking, it's a condition that could contribute to the overall symptomatology and should be considered in the differential diagnosis.