Upvote:4
Since Haneda to Kitakyushu is a domestic flight, your port of entry will be Narita, where you will need to go through immigration before you can proceed to Haneda.
However, as far as I'm aware, Japanese visas don't usually indicate a port of entry or restrict you to one. So it should be fine to enter at Narita and then continue on a domestic flight, even if you originally mistakenly stated Kitakyushu as your port of entry when applying for the visa.