I went for a quick and temporary fix of...Waterbug, can you guess? Goop.
And because I went so far out on a limb it will probably work.
I must confess...I use goop too. When a rock pops out of mortar I epoxy it back in place.
Did the pet store test KH & GH?
The water seems to be getting a little more clear on its own with just running the pump an hour or so per day. The air and water temerature is still fairly chilly in Portland. The daily high temp are in the mid to upper 50s and overnight lows are in the mid to upper 40s.
You don't mention the actual water temp., Air temps don't matter. Here's a little pond trivia, Google “Aeromonas Alley”. There's a water temp range where a bacteria can get the upper hand before the fish immune system is fully working. I mention this because your pH is so low. There could be a problem with the water which could stress fish while in “Aeromonas Alley”, Double whammy.
The 0.25 ppm ammonia is also an issue. Might have been from declorinating the water, but it's still there. Most people will tell you any ammonia is bad, and that's basically true. But it's more interesting than that. A bit more trivia if you like, Google "ammonia vs ammonium". And there are
charts where you can tell how much of your reading is safe ammonium, and how much is toxic ammonia. The test can't tell the different, hence the charts. You have very low pH (off the charts low) and I'm guessing pretty low water temps, so you may actually have 0 ammonia. How's that for trivia?
In other threads I've been writing about pH crashes and pH buffering...if you decide to ever go that route you have to be careful in the timing. Raising pH will convert some ammonium into ammonia and that's a problem. You might consider pH buffering before the water gets warmer and there'd be more ammonia issues.
It is still raining quite a bit. Do these conditions affect the water quality readings? Should I go a few days between feeding them?
The pH of rain in your area averages 5.3 to 5.5 (not sure where you are exactly). Can be lower, can be higher (but well under 7.0). A lot of rain, maybe a thunderstorm (3 and 4 pH possible) coupled with low KH and you could get a pH crash and then pH swings.
I wouldn't be feeding the fish with ammonium present and at what I assume are low water temps (guessing).
I'll pop just one more thing in your ear if I might...at a pH below 6.5 Nitrosomonas bacteria (ammonia converters) don't reproduce. They also require a carbon source normally measured in KH. I can't predict the future but it seems like you could be in a bit of pickle. The only way you'll be able to control ammonia, as water temps increase and if pH stays below 6.5, is with water changes. That's a tough road imo. For you and the fish.