I've a custom made map with a bunch of monuments and a ranch, all NPCs spawn in fine. 

Then I've adjusted the map slightly by adding a fishing village and updated it's name, then manually adjusted the .sav files to also have the same map prefix in the name. Everything loads in fine and player bases & items remain. However there are no NPCs or sentry guns in the fishing village. 

Is this because I messed around with the .sav files, my guess is they store the NPC spawn points that it generated at some point, but won't pick up newly added one.

Any ideas how to fix this are appreciated, otherwise ill just wait until next wipe to see what happens.

You will need to wait tell next map wipe or use the build plugin to manuly place them.