Hope this isn't too late to help you!
I thought I was in the same predicament, the trouble is base EU4's sometimes convoluted mission triggers. You don't actually need fungi in your capital, you just need to have a manufactory in every fungi producing province you own.
I'm actually stuck later down the path, I'd expanded outside the mountain's (blame the nobles for egging me on) and I need to get the average autonomy below 20%, which is going to be rather expensive given that I'd just been turning all of that into trade companies.