This information helps, thanks.
First on the swords not doing well: lack of nutrients, plain and simple. Echinodorus are very heavy feeders; if I do not dose Flourish Comprehensive twice a week mine develop yellowing leaves within another week. They must be fed. The recommended dose of Flourish (in a 55g I would use 1 teaspoon the day following the water change, and 1 tsp 3 days after that to spread it out. No more than this. Your swords will improve [unless something else is wrong that is not identifiable here].
Adding Excel is not likely to help. It is liquid carbon [and the store was correct, Vallisneria frequently disintegrate into mush with Excel] and technically should be similar to using CO2. But in either case, without sufficient nutrients to balance, adding carbon is not likely to help. It certainly will not help the swords unless you increase Flourish Comprehensive accordingly, and since Flourish is intended to natural systems I would not recommend using Excel as that sets up a different (higher) level of balance.
The single Life-Glo 2 will be sufficient light for the swords with Flourish twice weekly. The second tube, the Aqua-Glo, is unnecessary but as I mentioned it is half the intensity of Life-Glo so it is not actually adding much. But, it is increasing the light a bit, and in the absence of nutrients (Flourish Comp) the plants cannot use it, hence the algae.
I believe the above explains the plant/algae issue. Now to the more critical, the fish problem. Assuming nitrates are below 10, and with those plants I would expect nitrates to be low, that wouldn't seem the issue. And there should be no shortage of oxygen with those plants. And even during darkness, with so relatively few fish I cannot see the oxygen being low.
If the store numbers for pH and such match yours, and assuming they use a liquid kit, I see no issue there.
I would check the pH and nitrates regularly. Always test the approximate same time each day as both can vary during the day due to normal biological processes (in planted tanks especially), so always first thing in the morning, or at noon, etc. Monitor pH daily, at least for a full week after a water change. Nitrates maybe every other day for the week just to detect anything, if present.
I would also do a 50% water change every week, without fail. While the fish load is no where near capacity for all those plants in a 55g, this will not hurt. Clearly there is something toxic in the water. And a change using a good conditioner [in this case I would suggest Prime since it handles everything] should help whatever it is. Unless of course it is in the tap water to begin with. Do you notice any changes in the fish after a water change, that would suggest this?
Another possibility is something toxic like wood or rock. I went through this in 1997, fish kept dying and nothing could be found to explain it, until all the wood was removed; end of problem. One piece may have contained some contaminant and it was slowly leeching out over time. Any wood or rock in the tank? And what is the substrate?