I was struggling to get Far Cry 3/4/Primal working (Still working on FC3).. but I managed to get 4 and Primal working and so I thought I would leave the solution here for anyone else struggling with this.

Turns out the problem was, OneDrive.. OneDrive replaces your docs folder if you turn it on during installation, I had turned it off as it had caused me some game problems in the past, I thought I had fixed all of these problems and so forgotten about it. But no.. it came back for FC.. I keep backups of my saves/doc etc on my home server, so for me it was simple enough to go to switch those folders to new versions (see below) and copy and paste the files to the OneDrive save and profile location..

Educated Guess
If you don't have backups, you probably have to start from scratch.. I would assume If you rename the current folder to say 'Far Cry 4BAK' and then create a new folder called 'Far Cry 4', uninstall and re-install the game (I didn't have to do this but I image this might work as it has to re-create the files during the install)

But I know .. rename old folders bak> create new folders> add the backup files .. works.

I am still working on Far Cry 3.. which I have tried the above without any joy. It just sticks on the splash screen and has 'not responding' in task manager. I'll keep trying though.

Hope this helps.