Josh,
For a timer Done (DN) bit to stay on, the Timer logic rung must stay true, or "on". Use the Timer Enable bit to latch the timer on (self-latching), so that it does not self-reset. In other words, some condition starts the timer, but once started, it latches itself in with its own EN bit, until reset by some other condition (low level switch in this case).
If you are doing that already, then I would need to see the complete program (at least the section controlling the pump) for further troubleshooting. Could you post it here?
Your pump control should look something similar to this:
PS: I trust that you wired the power supplies in PARALLEL, instead of series. A series connection would give you 48 volts, instead of 40 Amps.