The original poster has made an important point though which affects all measurements of EW. To measure the EW of a line you need to establish where the continuum lies so you can measure EW relative to it. This needs to be done in a systematic, repeatable and reproduceable way. The problem here is that at this resolution we do not see the continuum. The overall shape you are removing here are actually bands of very fine unresolved molecular lines. If these change in intensity your pseudo continuum, and consequently your EW will change even though the strength of the line you are measuring may be unaltered. The solution is generally not to try to remove the continuum across the whole spectrum but to try to define a local continuum for the particular line of interest. Ernst has been plotting the EW of the H alpha line, perhaps he can describe the method he has been using in this particular case so others can replicate it.
Robin