I run into the same issue with my digital timer having limited on/off times. Mine has a total of 14 settings (7 on/off) cycles. But I also have 2 analog timers that have 48 settings (24 on/off cycles, with minimum on/off times of 30 minutes), I got those at K-mart. They are heavy duty lamp timers (15 amp), and were under $8 ea.
Also something I didn't mention that might help you is that because plants don't photosynthesize at night (in darkness), they don't drink up water during that time (no ware near as much anyway). So you don't really need to run the
pump until about 30 minutes before first light, and about 30 min after sundown. As an example I have ran a flood and drain system 30 on and 30 off all day long during light. Then at night I would cut it back to as little as one on/off cycle during the middle of the night (during summer as little as maybe 2 cycles at night) just to be on the safe side.