While waiting for permission to use the replacer, I tried some things and my current solution looks like this:

• Open MessageBox
• Inject Journal.swf
• In Journal Constructor, hide the MessageBox and disable the MB Button (and its ability to gain focus https://gameware.autodesk.com/scaleform/developer/doc/4.0/clik/gfx_controls_Button.html#disableFocus)
• Close the journal by calling GameDelegate.call("buttonPress", [0]);

It's not as elegant as the replacer and you always see the messagebox for half a second before the journal opens, but it should be 100% compatible with everthing, so I think I'll go with it.

Thanks for the input everyone. I wish I had known all this stuff when I started