Six weeks after that Jacob was still having trouble breathing and a camera inserted down his throat revealed it was about 90 per cent blocked so doctors performed emergency surgery to remove his tonsils and adenoids.
Not long after that he ended up with a gallbladder blockage which required another operation to insert a drain.
All that was before he was able to have the stomach operation he needed to put the organs, which were encased in a sac outside his abdomen, back inside his body.
"He's a tough little bugger," Craig said.
Three weeks ago he had his final operation and on Monday the family was allowed to go home.
All the while the Johnsons were staying in Ronald McDonald House and taking turns looking after Emma while the other stayed with Jacob.
"Having Emma too and having to take her to the hospital every day wasn't easy," Craig said. "Now she's crawling it made it even harder."
Being confined to a hospital bed for most of his short life meant Jacob had a way to go to catch up with his sister.
He could sit up but was a long way from crawling because he had been unable to lie on his stomach until recently because of the bulge created by his organs spilling out.
He had also not yet learned to eat or drink because he has been tube-fed since he was born.
But the Johnsons told the Herald they were just happy to be back home in Morrinsville.
"We consider ourselves pretty lucky. We got to go home with our children, a lot of people don't," Craig said.
Despite that, they admitted the past nine months had been traumatic at times.
"We had our moments. For me personally, if it got a bit much at times you just had to walk away and let the nurses look after him for an hour," Craig said.
"It was really frustrating and quite depressing," Selina said.
But being able to stay close to the hospital at Ronald McDonald House made life that little but easier.
"The people are amazing, the facilities are wonderful. We can't say how much we appreciated everything there," Selina said.
The Ronald McDonald House national appeal week starts on Monday.
The charity provides free accommodation and support for families with children in hospital.
Street collections will take place on Tuesday in the North Island and Friday, May 12 in the South Island.
How to help
Text FAMILY to 4483 to donate $3