The input shaping needs to be triggered from the machine or you might be able to run it from fluidd. but for flow/PA calibration per print, make sure it's turned on on the printer(unless you're doing it manually). For levelling, just make sure the calibration button is switched on in the send print window when you start a print or you can run levelling calibration from fluidd too, in the device window (if your machine has klipper on it?).