My initial reaction to looking at the data is

  1) It is undersampled
  2) Why are the synce pulses different amplitudes
  3) The raw data contains little or no information

It appears, although not clear from your comment, that there was an
existing system which weighed the trays. If this is the case what I
would do is connect in parallel and record the data.

I would send say 100 sets of trays through with known weights in. Say
10 with minimal and 10 with maximal and so on. Then keep a note of
what you sent and when.

Now you have a representative data set to create a logged file at say
44100Hz sampling rate and use that as a reference or perhaps use the
WAV recorder to create a simple raw record. Most importantly it has no
processing at this stage.

You can then use this to refine your processing technique. Later in
the projects life it acts as a system validation check. Some of the
ones I have created are the most important parts of the projects I
have worked on. From damage limitation (that's what the customer was
actually doing when I was called in). To, 'I can prove you have
changed something'. To 'Ooooops missed that!'

In summary
==========
I would suggest at this point you don't appear to have valid data.
Wether that's a result of hardware or undersampling is impossible to
say with the amount of information here.

Put some 'calibration' weights on and make sure the static levels are
what you expect from 0 to typical. Then move to dynamic at increasing
speeds.

You will no doubt need a calibration section in the design anyway!

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