You've made a lot of progress - the map looks great!
Since I have been going through the same process modding the Yamato Damashii SunnyDay map, here are a few notes based on the discussion so far:
The applicable map sections between the stock/extended maps are numbers 00, 01, 09, 15, and 24 (for both the 'WPEH' and 'WPEN' prefixes). What I did on my map mod was to create another layer on top of everything else, then I put copies of the applicable stock map sections into it. This layer can then be turned on/off in Photoshop to produce the stock or extended map variants.
This will be a bit more difficult for you to do since Chemkid had already produced both stock and extended versions of the map I was working with. You'll need to either re-blend the map or perhaps use a cloning stamp to extend the coastlines in the appropriate places.
The parts that change are:
1) the frame in sections 00 and 01 of the upper-left corner of the map.
2) The west coast of Luzon in the Philippines; the roads NW of Manila also change.
3) The western coast of the Malayian peninsula is extended.
4) In the Solomon Islands, the Shortlands base is changed to Buin and Shortlands is moved one hex south to the actual Shortland Islands.
It helped me to take the stock and extended versions of the v1 Yamato Damashii map and put them into separate layers in the same Photoshop file. Then zoom into an applicable section of the map and turn the top layer on and off to get an appreciation of the specific map differences. That might give you a better idea about how to best attack the problem.
As for creating a 'dots' version of the ocean hexes, I can help. I've attached a .zip of a Photoshop file containing the dots already masked for the map. Just import it into your Photoshop file and combine it with Chemkid's land hex mask that he provided in his latest map upload (the 600MB+ one). Then you can turn the appropriate layers on/off to create no hex, pure hex, or hex/dot hybrid versions of your map as needed.