The version of the Combined Replace Macro Set from Glorious Trainwrecks is not fully compatible with SugarCube (any version), so you don't want that version.
Read the included documentation. No, seriously, read it. There are differences you need to know about.
Open the included JavaScript (.js) and CSS (.css) files in a plain text editor (do not use a word processor), copy their contents and paste them into the appropriate sections (Story JavaScript and Story Stylesheet, respectively).
If you are trying to alter the width of the space to the left of the area that contains the Passage text then you need to use the #story ID instead of the body element.
Comments
The only problem is that I had this in my stylesheet:
#ui-bar {
display: none;
}
body {
margin-left: 3.5em;
}
and after adding the javascript, the iu is gone, but the margin-left doesn't work. It's like the ui-bar is still blocking it.