This is not aquaculture, or hydroponics, it is Aquaponics; and it has its own set of rules and requirements which are all about balance between fish and plants.
Beautifully said! Bravo! I think you should have this point in big text in bold and red or something!!!

Remember, the fish like their water pH high and the plants like it low.
I agree with the plants pH, but where do you get that fish like the pH high? Aquaculture research shows that aquaculture setups do well with high pH because the biofiltration is far more active, but the added risk of unionized ammonia offsets the the benefits if not properly monitored (which aquaculture facilities obviously are). Since it costs money to remove water from aquaculture facilities they would rather keep the pH high remove the ammonia than to have more frequent water changes that costs them money to dispose of. This is my understanding as to why pH is suggested high in aquaculture, but this is not the case for aquaponics... in general freshwater fish like a median pH of 7.... I could be wrong as I have not extensively read on the subject, but I never really questioned it because it appealed to my common sense...

The logic is that bacteria cannot live in a bottle for any extended period without oxygen and ammonia constantly being fed to it.
Oh they can survive just not reproduce. Sure some will die. This, among other experiments, are common in an introductory microbiology course. Believe me, the people who make this stuff know plenty about it, and you are getting living bacteria. Even if they are dormant, they will come back alive. Think activate dry yeast (which we are all more familiar with and can believe easier)

Do NOT use any animal urine, and especially not human urine, for these prolific sources of ammonia contain toxins, including prescription drugs (and perhaps nonprescription drugs) that you do not want in your Aquaponics system.
Okay, very good points, but you can use your own urine if you are not on any drugs (or smoke). If you carefully check what your drugs metabolize to, you may even still be able to use your own urine. You can always consult with your doctor for added wisdom. As far as disease, if you are the only one eating your fish and plants then it doesn't matter what disease you might have. Debatable, human pathogens cannot get into the systems of plants or fish, but again if it's just you go for it. Would you be worried about getting yourself sick? Of course not! Oh and yes, most people have arsenic, cyanide, and other nasties in their urine. DO YOU KNOW WHY? BECAUSE IT'S IN OUR WATER... YES, THE WATER YOU JUST PUT YOUR FISH IN. So who cares! The plastic and PVC pipes will leach far more carcinogens into your water and food than your urine... so it REALLY does not matter. Happy peeing folks!

If you have incoming water pH numbers in the eight plus range, then the best way to lower the pH is to use a reverse osmosis water filter.
If you are in a rush, sure that would work. My suggestion would be to set up your system with the tank, grow bed, and water. Start the pump and either seed the system with bacteria or let nature take it's course (just be ready to wait a month or two). Next, take a whiz in your pond, tank, or aquarium. Now, let the bacteria start doing their thing. As you mentioned, the bacteria will put hydrogen ions into the water thereby increases the acid content naturally. Take periodic ammonia and pH readings and pee in there some more as needed (you want to keep the bacteria producing hydrogen to lower your pH). Once the pH is where you want it (and to be honest a pH of 8 or even 8.5 is fine) put the plants in. The plants will start to remove the nitrates. You can wait until the plants are established in a few weeks or put the fish in right away.

With the addition of the Stress Zyme, we have not seen any continued build up of solids; and we have cleaned our grow beds more than once to remove the excess roots mentioned below.
I prefer using red wriggler worms. First off, they're cheaper. Secondly, it seems far more "organic" than buying something in the store. Third, doesn't the bottle say not for use on fish for human consumption??? The bottle at my Walmart does, but I am guessing they carry a different brand at your Walmart. I will snap a picture next time I am there of the container for comparison. Oh, I was just digging up plants to remove from for the new growing season, and the handful of worms I put in last season have multiplied aggressively. Every plant had roots covered in fish poop and WORMS! The worms were SO FAT AND BIG. I have worm bins set up, and I have rarely seen worms the size that all of these were... Needless to say, they were happily chowing down on fish poop and sludge, and they like to stick around the roots for some reason, which is GREAT for the plant, just GREAT. Also, worms are home to hetrotrophic bacteria in their intestinal tract.

Notice I said basic (base), not alkaline. Some would argue that they are the same; but in dealing with pH and water quality, there is a difference. Alkalinity is a measure of the alkaline buffers found in the water. These alkaline buffers are dissolved minerals, like calcium, that keep the water's pH at a higher than neutral seven pH. Any attempt to lower the pH of water by adding in an acid (pH down) will be countered by these alkaline buffers and not allow the water's pH to change and go to a lower number. You might see a sudden change after adding in an acid, but it won't last and will soon rebound back to its higher pH value as it is absorbed by the alkaline buffers. You can keep adding acid to your water until you have saturated the alkaline buffers, but understand that acid + alkaline -> salt + water. What this says is that you will end up with is a more neutral pH and salty water.
I can't agree with this paragraph based on my knowledge. Your chemistry here is a bit vague and frankly sounds a bit mystical? Are you saying that despite the concentration of alkaline solutes in the water, anything that is an "alkaline buffer" will keep the pH high (in other words infinitely, irrespective of concetrations)? If anything, I would say this has to do with the media in the grow bed or some other material that the water comes in contact with that starts reacting when a certain level of pH is hit. As you know, egg shells or other shells are commonly used as natural pH buffers because the surface area to mass ratio of these items are low, but the reaction with the water as pH lowers increase (exponentially by a power of 10 per pH point) thereby giving a maintenance free method of controlling pH assuming a slow change. However, we unwittingly might use a grow bed media that act in a similar fashion thereby preventing us from getting the pH we want and because there's so much media this could be a near infinite source of "alkaline buffer" for all practical purposes... which could be what you have observed.

I like how you've understood the differences and implications between basic aqueous solutions and alkaline solutes (salts) in solutions. This needs its own section because pH is quite important... or at least expand and reorganize that information. I can't stress this enough, but pH is the single most critical variable to control in your system. The single most. I can't stress it enough. Single most...



SIDE NOTES:
The aeration pumps we use draw from the ambient greenhouse air, including the added CO2, and feed it into the fish tank water. This extra CO2 mixed with the water creating carbonic acid, and the pH plummeted all the way down to 5.8.
I had written a bunch of information on carbonic acid before reading the subsequent paragraph which supports your claim that it was in fact carbonic acid in your water. I did not believe your CO2 concentration had risen that high, but since you have shown that is the case, I would like to change my statements to warnings regarding CO2.

If your CO2 was high for extended periods of time, the concentration of CO2 in the air would be TOXIC to your plants. Also, if you do not actually monitor the spike in CO2 you can get LESS yield from your plants, which is NOT what you want... I have the paper somewhere that goes into it from my archives, but for now I site this as evidence: http://www.ncbi.nlm.nih.gov/pubmed/11540191