Though is a conjunction here as it's linking the two things. You could change it to 'but only': For "Is" and "Is-Not" but only with Rule and Line, The object of define is basically everything before it: I could define "Is" and "Is-Not" with rule and line and "Up-and-Down" without rule and line.

Just so you know - this is poetry, and old-fashioned language. It's very difficult even for native speakers to make sense out of this.