When your wife is IN New Zealand again, as long as she gets back before her travel conditions run out, there is no urgency to apply for anything, because for someone inside the country, a Residence visa lasts for ever - it's only the travel conditions that have a two-year life.
You're quite right that her travel record at the moment will not make her eligible for PR.
https://www.immigration.govt.nz/new-...anent-resident INZ count BACKWARDS from the date of application, so she would need to apply at some time when, in the 12 months leading up to that time, she had spent at least 184 days in the country, and the same in the 12 month period before that as well. (The first year, when she was there, would by that time have slipped out of the reckoning, because it would be more than two years before the date of application.)
Depending on counting exact days, she MIGHT be eligible for a variation of travel conditions
https://www.immigration.govt.nz/new-...vel-conditions, which would get her another year when she could travel outside the country and return.
But if she doesn't have particular travel plans when she comes back, she doesn't need to apply for that. She could just wait till she can show two years immediately beforehand when she meets the 'time in NZ' criterion, and apply for PR then.