Finding peak height with all the various image processing filters and signal processing algorithms has been time consuming. I think there is one filter which will always have to be analyzed initially separately. That is, the limit range filter that gwyddion uses, and that also occurs in other image processing programs (i used it just twice in GIMP). The peak height for the N term (center tall peak in each hexamer) is highly significantly reduced when the limit range is used. All other processing filters and algorithms seem to produce a relatively even group (when Y is normalized to a percent). Initial data of the comparison is below. You can see there is one value (max 101) which i need to find. There are no perfect datasets, but the shere number of plots represented here means finding it will do nothing to change the outcome.
Here are each of the four dodecamers (traced as two hexamers).