To enter Nepal won't be a problem as you can get a visa on arrival. Or if you have some sort of Indian ID from earlier such as PAN Card or Voters id from when you lived in India you can just show that in which case you won't require a visa.
I called the pakistani emabssy in Kathamndu and they said that you can apply for the visa here but it may be reffered to the Pakistani emabssy in Australia. Maybe easier just to get the visa for Pakistan in Australia itself.