Word-final characters

Is there a way to set your font to automatically use different characters when they appear at the end of a word, e.g. Greek sigma?

Also, does the latest update allow you to make conjunct characters? All I could find with a search was people saying several months ago that you couldn’t with the then-current version.

No. Font Creator doesn’t yet support Open Type features. You might be able to do what you need with Autocorrect. There are some free tools from Microsoft for adding Open Type features to Truetype fonts.