Here is how I do it:
Take the initial image with PSP. Display the palette, make screenshot, save as bmp.
With PEdit, open an existing palette, where all the civcolour are cyan (for instance), so you know how to avoid them.
Open the bmp of your 256 colour palette. Then reassign the colour to the PEdit palette.
I can help if you want.
Also, you made Nara period (710-794), that would fit well for early medieval era in my mod, and are making Kamajura (1185-1333), suitable for late medieval era. But what about the Heian period, from 794 to 1185? It would be nice for the intermediate high medieval era.
Also, any progress on cavalry? Tell me if I can help, I'd like very much to add Japan and Egypt next in my mod. And... If you could make settlers and workers to accompany the military units, it would be really great.