Sorry I misunderstood your second point, but glad to be of help.
You are correct that Scaler is all about identifying a chord sequence. If you want to alter the timing of chords you need to look at Playback Timings on the EDIT page.
Having said that you may want to look at this topic on Using Midi Clips to Control Scaler, which is my preferred approach to controlling Scaler. I think this is what you may be looking for as you can control Scaler either from a midi clip or from a midi keyboard.