You do need to restart the story to get the "for" or "against" Jozic achievements alogn with the options of signing and riddle choices. I know when I restarted, that was the map that was only available on the main menu when I saved later and came back. However, since I am new to the game, I didn't care if the old saves were there. Still learning all the ways I can optimize and lay tracks.

However, my understanding from what I seen game wise, saves in Jozic can be loaded in the full version so they must not overwrite , but don't quote me.

In the full Rail Route you can play the full Story of Jozic just by starting the Prague map from the beginning ('Play' button on the map tile). Your old saves are not overwritten, is suggest renaming the last to something reasonable to find it later once you finish the story.

However, older autosaves are deleted on per-map basis.

I'm not exactly sure how to get this achievement... When playing Prague, there comes a point when he asks you to join him and go to Wakefield and get a high score there. I did that, and that seems to be were the story ends. But I never got the achievement. Is there something else I have to do in order to end the story?

The story should continue for another couple of hours after Wakefield. If it does not, please submit a bug.

Jozic showed you how to buy platforms, add track and sign up for contracts. If you keep improving your network, he will come back and take you through the next stages.