The Highlight toolbar item was actually the first thing I worked on for 3.1. I had actually tinkered with it during the 3.0.1 development stage but had disabled it for the 3.0.1 release build. Before the 3.1 alpha release I added the code back in but forgot to put it in the big list of toolbar items. So it's there, but you just can't pick it. So that's useful. :-) I'll fix it for the next alpha but you can make it work right now if you want.
1. Open your preferences file in a text editor (like TextEdit or BBEdit) or even better a dedicated property list editor (like Property List Editor, including with Xcode).
2. Find the line that says "NSToolbar Configuration." If you've never customized your toolbar, this won't be there so you should make some change first, however insignificant.
3. Under the Configuration key is another key called "TB Item Identifiers." There is a list of strings under that.
4. Make a new line in between one of the strings and add this line: "<string>HighlightIdentifier</string>" and save the file.
5. Launch MacJournal and you should have the Highlight toolbar item.
You can Command-Drag it around wherever you want, but if you drag it out you'll have to edit the property list to get it back again.