Improvements to the itc setup scripts.

Resolves #2, #3, #4 

Regarding #2
@jchodera:  I just wanted to make sure if I understood this correctly:
 Are the the ChoderaHostGuest and ChoderaWaterWater protocols we defined last time .inj files?

Regarding #3:
I had to reverse the Buffer to Guest titration with the Host to Guest titration to have the scaling factor available.   If this is undesirable, we might decide to define in this order, but add them to the experiment set in reverse order. 

Regarding #4:
I just added a water water protocol, but using the buffer troughs. Would that suffice?