Quote by ollo
If I know the temperature of the material I'm looking at and I know which transition I want to look at how can I calculate what the observed flux (in Jansky) should be?

You need to solve the radiative transfer equationin particular, finding the
Einstein Coefficients
Quote by ollo
Also, what can I calculate from observed FWHM?

The width of lines tells you many things concerning the cause of
Line Broadening