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What kind of time cycle should I be looking at for flooding my system and draining it?
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Well that can be both complicated and easy at the same time. The easy answer is on just long enough to flood the system and wet the roots, then off. The complicated answer like always has many variables. like air temp, system design, amount of
growing medium, type of growing medium. As well as like you said plant type and size. Also the timers available settings are a factor to how you set it.
I would start out trying 30min on and 30min off, or (better) 15min on and 15min off (if the timer allows it). Keep an eye on the growing medium (you don't want it to dry out). If the plants wilt at all they are drying out (and/or water temp is too high). Disease can also cause wilting, but we'll just assume that's not a issue at this point. Basically just keep an eye on the plants and watch for singes.
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Is it best for my aerators to be on constantly, or is it okay for them to be on the same time cycle?
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24/7 is best, but if not possible just have them on as much as possible. Also going by your bucket design from the other thread, assuming you are planing on designing it so there will be water/
nutrients in the bottom of the buckets all the time, I would suggest putting a air stone directly in each bucket. That would be better for the roots that are submerged as well as the ones that are not.
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I hope to grow a Tomato plant and a batch of Spinach if they will work together in the same nutrient solution while still being in separate pots.
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I don't see why not the both have the same pH requirements, I would aim for 6.0 but if it fluctuates a little either way (5.5-6.5) not a problem.