low spongy brake pedal is usually caused by the fluid in the lines and the lines themselves and sometimes by the pad. (this is excluding for the fact a crappy master/slave). if it's a disc and drum setup, a improperly adjusted drum will also cause that feel.
and input shaft won't lead to a slipping clutch. it'll cause noise and probably rough shifting. a worn input shaft bearing also won't cause that either, just a lot of noise.
as for your first question, it depends on the scan tool you're using to view freeze frame data.
most will tell you the cylinders (through cylinder ID, or misfire counters, etc) and it'll usually say the position of the gear shift too in a separate category. depends on the car, and the scan tool.
this is from personal experience at work. there could be more things.
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