I am attempting to calculate back trajectories for event based precipitation samples to trace sources of atmospheric pollutants (mercury, nitrogen, pesiticides). I am uncertain as to what height or pressure I should use in the model. Most of the events I am trying to model are summer thundershowers. Also, my site is located in rugged mountainous terrain in Colorado at an elevation of 9500 feet.

We have two frequently asked question pages that is very similar to what you are asking. They are at:

Generally what has been done in the past is to pick several levels near where the precipitation is formed, which is generally between 850 and 700mb. However, since your location is already at about 700mb above sea level, you will need to do some above 700mb to account for the terrain.