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Excellent news!

Yes, duty cycle is the correct pin.

Is the frequency reasonable and the valid bit set?

It sounds like the EDM output is single ended which means:

1. The EDM duty cycle output should connect to TB2 pin 13 (IDX+)
2. The EDM signal ground should connect to TB2 pin 15 (7I96S ground)
3. The 7I96S IDX input should be jumpered for TTL mode (W1 left)
4. 7I96S IDX- (TB2 pin 14) must be left unconnected

Note the if you connected the inputs to TB2 pins 13 and 14 without a ground
and ran the EDM system you may have damaged the EDM output or
7I96S input.
 

I should have explained more.
point = [wx, wy, wz]
if not self.plotdata or point != self.plotdata[-1]:
self.plotdata.append(point)
This adds a plot point. We would need to change it to also add color.

point = [wx, wy, wz,color]
or maybe better:
self.plotdata.append([point, color])

then later in the file:
#GL.glColor3f(1.0, 0.5, 0.5)

GL.glBegin(GL.GL_LINE_STRIP)
for p,c in self.plotdata:
GL.glColor3f(*c)
GL.glVertex3f(*p)
GL.glEnd()

a few other initialization and clearing details to follow up. but that might work.