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Is there a way to stretch the captured waveform without amplifying it at the same time?
Yes. Use the magnifier tool and make a frame as tall and narrow as you can. This will expand the capture only horizontally.
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Also, can I superimpose a captured reference waveform on a running screen so I can compare waveforms visually?
Not yet.....

PicoScope 5 has composite overlay but PicoScope 6 does not have a function like it yet. It would not put it on a running screen though....just superimpose two saved captures.