Why would you want to do this? Lets say you enjoy the Tokugawa and their ninja bonuses, but you want the ninja resource in your capital. Lets say you like the Chosokabe, but hate capturing Buzen to make your sweet ass archery range for the accuracy bonuses. Now you give your home city the good resource you want.
Make yourself a new mod by using the pack manager. All you will need to add is data/campaigns/jap_shogun/startpos.esf
Once inside, navigate to CAMPAIGN_STARTPOS -> CAMPAIGN_ENV -> CAMPAIGN_MODEL -> WORLD -> REGION_MANAGER -> REGIONS_ARRAY -> [find your region]
The regions are numbered 1-67. Use this info to help yourself remember where your region is.
When you are in your region specific array, navigate to REGION -> REGION_SLOT_MANAGER -> REGION_SLOT_ARRAY
The arrays inside here are the data tables for the building slots you see in game. Generally speaking, it goes:
0-4 - Generic
5 - Castle
6 - Rice/farms
7 - Port
8 - Special resource
Navigate down to the final BUILDING level of the bottom one, you'll see 5 lines. I have no idea what the first two lines do. The third line is the building ID. This is what you'll be changing. The 4th is the owner, and the 5th doesn't really apply to Shogun.
The third line will be one of these, and they are self explanatory:
SHO_Region_Specialty_Craftwork_1_Artisans
SHO_Region_Specialty_Iron_Mining_1_Iron_Mine
SHO_Region_Specialty_Stone_1_Stonemason
SHO_Region_Specialty_Smithing_1_Blacksmith
SHO_Region_Specialty_Horses_1_Pastures
SHO_Region_Specialty_Intellectual_Centre_1_School
SHO_Region_Specialty_Holy_Site_1_Holy_Site
SHO_Region_Specialty_Gold_Mining_1_Surface_Mining
SHO_Region_Specialty_Naval_1_Merchant_Colony
SHO_Region_Specialty_Timber_1_Lumbercamp
SHO_Region_Specialty_Ninja_1_Hideout
Change these around as you see fit. Thats it!
I'm pretty sure thats it. Hopefully this helps someone.