The negative testing is reassuring as it would have picked up many of major diseases.
A negative CT scan and MRI would make a hernia less likely. A physical examination by a surgeon can further evaluate whether a hernia is present. If so, surgical correction can be considered.
Regarding the protrusion, it can be an infection, abscess, cyst, or other skin condition. If this is considered, a referral to a dermatologist or surgeon can be considered for biopsy or drainage.
As for further studies, I cannot recommend anything more than you have already had done.
These options can be discussed with your personal physician.
Followup with your personal physician is essential.
This answer is not intended as and does not substitute for medical advice - the information presented is for patient education only. Please see your personal physician for further evaluation of your individual case.