I don't see the place for the step-up, you would need a step-down to power the pump.
You could use a 1S3P configuration instead of the 3S1P, use the step-up for the module,
and run the pump with the 3.2 to 4.2 cell voltage.
Test if a single cell gives enough performance.
With a single 3000 mAh cell, you can expect 5+ hours of runtime (a crude estimate).