A laparoscopy found fragments of endometrial tissue growing outside her uterus. During the operation Penney's appendix was removed, as is standard medical practice.
Penney says she was later told she had "a little bit of endometriosis" but not that it was causing the pain, so she was still in the dark about what was wrong.
Not long after the operation, an infection set in. Penney was in and out of hospital with septicaemia, along with an ileus - a paralysed bowel.
Surgeons eventually discovered the infection had caused adhesion around her uterus. To be pain-free, she was told, she needed a hysterectomy.
"I was 25. They said I couldn't have any more children - it had ruined all of that," said Penney, who at the time had two boys.
But just days before the operation, Penney was stunned to discover she was pregnant. The hysterectomy was cancelled, against the advice of at least one doctor.
"They said it would be a very scary pregnancy because they didn't know how the uterus would grow - but he's fine and healthy."
In July last year Penney had a full hysterectomy - the removal of her uterus, cervix and ovaries.
The hysterectomy eased the pain but Penney still felt awful. Digestive issues like bloating were so painful that she would make herself vomit to ease the pressure.
In December 2017 Penney used health insurance to go private, to the same surgeon who had seen her at Whāngārei Hospital, Mr John Lengyel.
She asked Lengyel to test for Crohn's disease and Coeliac disease. Blood tests turned up negative but Lengyel had his suspicions and asked for a bowel biopsy for Penney.
It came back positive for Coeliac disease.
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Penney said she had no qualms with the hospital or staff, who provided her with excellent care. But she wishes she had known more about Coeliac disease - enough to ask for a test years ago.
She had had chronic iron deficiency, eye problems and alternating constipation and diarrhoea for years, but never realised those were symptoms of the disease so didn't ask for a test.
"I learned how lucky I was that I had a good doctor when we went private. He believed something was going on and looked into it."
Her third son Grayson is the shining light in four years of hell, but Penney wishes she could have had more kids.
"I wanted a big family - even now, I'm still grieving," she said. "That's part of the reason I'm so angry - but we're very lucky we've got Grayson."
Northland DHB chief medical officer Dr Michael Roberts expressed his sympathy for Penney's years of pain.
The complications from her operation, and resulting hysterectomy, were "very unfortunate" , he said.
"Emma is absolutely right to recommend that patients should share with doctors their thoughts about possible diagnoses. Decisions about investigations and treatment should always be made jointly by patients and their doctors after careful discussion and consideration."