Have you checked your data if there is an interference between channels? Simple ground one input at the time and see a data log, if there is "0" leaking in the neighboring channel.
Looking at the diagram, my understanding that green line represents an envelope of the signal. You can't get envelope using LPF, as the nature of your input a noise similar, or AC signal. First of all, you need subtract DC offset from your data ( offset is a value w/o a signal), than you may run averaging or similar LPF filtering using squared up values ( x^2).