Two hundred feet is a long way. It must be adequately shielded. Ground the shield at one end only. The signal itself doesn't necessarily need to be grounded, but that depends on your referencing, of course. Differential is best. One of the most common noise sources is power lines- check for n*60Hz frequency content. Also, if you run goes by motors, coils, etc. More distance is best in this case.
The wires you run should be the same for both legs- length, gauge, and material. Each wire junction you create becomes another thermocouple junction; as long as they are equal it will be OK. Make sure they are solidly connected (you'll see an offset here more than noise).