Set the timer so that the CO2 comes on, say, 90-120 minutes before the lights come on. That allows you to saturate the water with CO2 before the uptake demand starts. When the light goes on, if there is sufficient CO2, photosynthesis can begin at peak efficiency immediately. Then, set the timer so that the CO2 shuts down anywhere between 2-5 hours before lights go out. CO2 is critical in the morning but less so in the afternoon. This strategy allows you to use much higher injection rates - but be careful in setting the rate so that you don't gas your fish.
Ray,
Photosynthesis is an energy conversion mechanism. The process converts photon energy directly into electrons and results in something called The Electron Transport Chain (ETC) which is a path along which electrons in the chlorophyll are liberated by being struck by photons - this is effectively electricity. So when you turn the lights on you are basically "plugging in" the plants to an electrical outlet. Higher wattage light means high numbers of photon collisions with the chlorophyll. This means a high electron ejection rate and therefore higher electrical current along the transport path. High current then requires higher nutrient/CO2 uptake to produce higher levels of the phosphate sugars that plants use for growth. As you mentioned, a nutrient or CO2 deficiency under this high electrical loading breaks the system because it affects food production rate. Of course, if this failure continues for 12 hours then yes, more damage is done than if it occurs for only 8 hours but the damage is being done by the intensity primarily.
On the other hand, plants consume the energy they produce and there is a minimum electrical current required to produce sufficient food just for the plant to live. Therefore it is entirely possible that the light energy can be too low, which means the food production rate is less than the food usage rate. When production equals consumption this is called the Light Compensation Point (LCP). When the light energy is only at the LCP the plant hangs on to existence by a thread and it won't matter how long the duration of the photoperiod is. If the light falls below the LCP the plant is doomed, again it won't matter how long the duration is because every second of energy produced by the light is lower than the energy being consumed during that same second. This is another reason why "siestas" are such an illusion. When lights are off the plant cannot produce food yet the plant is still consuming food that it produced previously so energy reserves become depleted. Therefore photoperiod duration is only relevant within the context of the intensity energy. Insufficient light energy cannot be compensated for by increasing the duration. Excessive intensity is exacerbated by longer duration certainly, but again, is only marginally mitigated by lowering the duration. So if you do a midday burst but if your CO2 is poor during that burst period you are doing damage throughout the duration of that burst.
It's difficult to judge circulation patterns without being able to visualize with a dye or some other aid. Do all or most plant leaves rock slightly? If there is debris in the water (such as leaf particles) does it have a tendency to head towards the substrate first? If yes to both of these questions then your flow rate and circulation are generally good. I'm normally having to clean the carpet plants regularly because that's where most debris head towards and gets caught. While this is annoying I consider it a good thing since it means I have good flow to the carpet plants. If flow is middling to poor then CO2 and nutrients have a difficult time being exposed to the plant leaves adequately and you wind up having to dose/inject more than you think necessary because of this inefficiency. Play with various placement of the spraybars. In my tank the optimum placement of the bars is a horizontal line across the back wall with all holes pointing directly towards the front glass. The flow strikes the front, is deflected down then travels aft and up along the back wall. This may not work in all geometric configurations but is a good starting point.
Cheers,