"No variables in Z-matrix" error in scan calculation of Gaussian
Ok, so I guess I'm on the right way now. Trying to fix such a complex system is always very difficult so what I did was using a similar system, I got one sodium atom instead of your NT and I'm moving the benzene away.

First of all: you got two different dummy atoms in there, atom 1 and atom 9, which I guess makes some problems. Also the extra lines between the sections are a problem. 

So here's the input for this, for a first try just from 2.5 in 5 0.5 A steps which at least runs without any errors:

# opt=z-matrix hf/3-21g

Title Card Required

0 2
 Na                 0.00000000    0.00000000    0.00000000
X 1 R1
C 2 XC 1 A1
C 2 XC 1 A1 3 60.0
C 2 XC 1 A1 4 60.0
C 2 XC 1 A1 5 60.0
C 2 XC 1 A1 6 60.0
C 2 XC 1 A1 7 60.0
H 3 HC 8 A2 2 180.0
H 4 HC 3 A2 2 180.0
H 5 HC 4 A2 2 180.0
H 6 HC 5 A2 2 180.0
H 7 HC 6 A2 2 180.0
H 8 HC 7 A2 2 180.0 

XC=1.39893
HC=1.09100
A1=90.0
A2=120.0
R1 2.5 S 5 0.5


So here's the point. The format basically needs to be exact like this. Everything else will confuse Gaussian. You can substitute the "Na" line with your cartesian coordinates, but then the numbering in the z-matrix section changes! you have to adopt those numbers. Oh and of course if you got a more complex system than one atom you want to not only define the distance of that dummy atom but also the angles, so it's in the right position. You might also need to adept the whole matrix so the benzene has the right orientation in relation to the NT, so at least three atoms in there need to be somehow defined by atoms in the NT.

If you want to have fixed coordinates (what you labeled as constants) in the z-matrix, you can add them after a blank line just below the last section.


  However, after a test run I'm not sure if it actually scanned that one
  coordinate, I just get one structure right now, I have to check how to
  do the scan correctly.


It works after adding that one 'S' in the coordinate which needs to be scanned.