I found the issue Tommy was talking about below. You forgot to set the Work Rate for the Cosmographer.

For you or anyone else who wants to fix this in their version, it can be easily done by going to ProtugalManuell_GameDefines in Core add adding it to the Insert Into Units section.

so change
PortraitIndex)
to
PortraitIndex, WorkRate)
and
'JFD_PORTUGAL_MANUEL_I_ICON_ATLAS', 2
to
'JFD_PORTUGAL_MANUEL_I_ICON_ATLAS', 2, 1

Wow. Some civ you got here.

Great mod! However, I was not able to expend the cosmographer in order construct an academy. It would say that the cosmographer used his movement points, but nothing would ever happen beyond that. So I was forced to send them all across seas and trade away the useless citites.

it's not showing up on my mod list for some reason

Dude, this is great, but where is the CID crime/organized crime component you said you were gonna release, been waiting for about 4+ years now

This looks like fun, time to go colonizing