should be destined for at least a 55 gallon, soon, or rehome them and get something else for the 29. At maturity, think of this fish as basically a "football with a tail" as a friend described them. This is the size of the lumbering comets that live in lake michigan off of navy pier, begging scraps from the tourists.
Meanwhile, 5 gallon water changes have led to that nitrate issue. I would not hesitate to make twice weekly 50% water changes your new routine until you situate them in a bigger tank. Start slowly with daily or twice daily 5 gallon water changes if you have not done one in a while. I don't want you to kill the fish or stress them further with an abrupt change of hardness or pH. Going forward, large frequent water changes will only help these fish. I wouldn't bother to test for nitrate for awhile, just keep changing water. After you have done several days of smaller and frequent water changes, ramp up the amount of water you change.
I would expect that the bloating is some type of internal infection. Assuming the fish is eating, treatment would require the use of medicated food. I don't have a source, but I know they're out there. Or the bloating could indicate this fish is a gravid female, and I suggest that because two months with an internal infection seems like it should have resulted in a very ill fish by now. The asymmetry is peculiar, but possible. If he/she is active and eating, there's yet hope. I would vary the diet to include some green foods, maybe occasional frozen foods. I personally believe color enhancing foods are unnecessary. You can keep feeding the pellets, but try some other things for this fish.
Darkening mouth color could be related to disease or simply a color change that many young Goldfish
go through. If it's the former, probably broad spectrum antibiotic/antifungal medication is in order. If the latter, enjoy it while it lasts. Black often shows up on paler-bodied Goldfish
but is a rather unstable pigment and usually leaves as quickly as it came. It is pretty typical to see dark pigment appear on the mouth, so I believe that's what it is.
I just re-read your post: Four and Six inch fish are way too big for this tank. The five gallon water changes were probably not keeping up with the waste even when you were doing them. I would work on the water right away. Yeah, you can add some salt if you want, but for the sake of the unaffected fish, correct the nitrate problem.
Better water, better food, bigger tank.