You are mixing a distance measure, versus a liquid measure. Does not compute! CC's can be converted to ML. If the level of measure were whole ( i.e. nothing in the chamber but fluid), you could calcuate the amount of fluid in cc's or ml it would take to fill that 5mm height space in a 43 mm fork tube. Actually, a very easy calculation.
I can only give the explanation and not a solution for your problem, because, unless I am mistaken, the rod is taking up some space with the tube that is being filled. With the measure of the tube, you could then subtract the difference of the rod measurement from the solution that would appear from above, and you would have your answer.