#Probe Points in Resonance Tester
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Besides including the input-shaper.cfg you also need to define probe_points in the [resonance_tester] section for input shaping, since it doesn't know your printer size without that. You should uncomment the [resonance_tester] section in your printer.cfg and also uncomment the right probe_points for your printer size.
I am not seeing an input-shaper.cfg.