I'm not answering in order asked, but:
1) ksandness is right. Do some research first.
2) Tokyo and Kyoto are awesome in July. If you like extreme humidity and random torrential downpours.
3) Worry less about which Tokyo airport and see if you can swing an "Open Jaw" with one end at NRT/HND and the other at KIX/ITM. It will save you the cost and hassle of backtracking and give you more time on the ground in both places.
4) Please please do some research. You could type in "Tokyo Kyoto honeymoon" in google and probably get 500 blog hits full of ideas.