How to merge transitions? I need to represent my signal as a set of transitions from one level to another, and I am interested in transitions that have relatively big amplitude 2000+.

I applied median filter to get rid of the high frequency part of the signal and result looks like this. Now I can take gradient and get set of transitions, and based on the magnitude of these transitions, keep only big one. So, I will get transition, corresponding to the left side of this peak, I will filter out transitions from the top. But I would like to have right side of this peak also to be represented as one nice 2000+ transition. But as you can see on the picture, there is small kink in the middle of the right side that will break my transition into 2 parts. 

Is there some kind of a filter that will transform my signal and remove this kink?
One of many possible algorithms to provide such edge sensitive information to its users are classified under change-detectors. The one that best fits to your kind of data uses thresholds, accumulators, memory, leakage and smoothing factors as well as variance and mean normalizers to decide on which changes belong to meaningful edges and which are just local variations.