Axie update: Mudkip seems stressed

Hello all,
I have now had Mudkip for about two months and up until a few days ago, it's been doing great. He/she eats like crazy and has grown from 2" to over 4 inches since buying him/her.
Because I hadn't cycled my tank before putting the little Axie in it, my ammonia levels have been increasing despite my 20% daily water changes and once-a-week 50% changes. She has two Bio-filters and two ghost shrimp to chase (he/she is quite active and loves hunting) as well as to help clean up after her a little bit.
However, after a couple weeks of having the shrimp, the ammonia levels have continued to sit at 0.5 - 1.0 and her nitrate/nitrite levels remain at 0 so her tank still has not cycled it would seem. A few days ago I purchased Prime to help combat the rising ammonia and have been adding 1mL every morning with her water changes (this is within a 10 gal. tank).
Since adding the Prime, both ghost shrimp have disappeared, this may be because my Axolotl finally caught and ate them, but I am doubtful that this is the case because she has never before been quick enough to nab one. I suspect that the Prime is the culprit in killing the ghosties, and she simply ate them after they died. Mudkip eats EVERYTHING. She even began eating her own poo, which is quite gross but I've read that this is normal behavior, however I'm wondering if it is because I am not feeding her enough? She will readily gulp down nearly two whole cubes of blood worms and has eaten a large section of earthworm once but that experience wasn't the most pleasant for her I suppose because she refuses to eat any earthworm now. Her water temperature sits a bit higher on average these days (63 degrees Fahrenheit) due to the warm summer weather, so I continuously put 2 liter frozen water bottles in her tank throughout the day to keep the temps at a cool 57 degrees Fahrenheit.
The thing I am most worried about is the flicking of her gills that has commenced in the last couple days. Previously, Mudkip was extremely active and loved exploring her tank, but these days she will just sit motionless in one of her hiding spots and flick her gills for 5-10 minutes with approx. 5 second intervals between each gill flick. She still eats all of her food but has become quite lethargic and her tail does seem to curl when she's not swimming around. I've read that this is a sign the Axolotl is in discomfort/pain, could this be because of the Prime? From possibly eating the ghost shrimp? The ammonia? Or maybe the temperatures?
I apologize for the essay, I realize that these aren't extremely dire circumstances, I'm just concerned for my 'Lotl and getting some direct advice from you all on what the problem really is/what I can do to improve my tank and my Axie's health is always the most helpful solution and I want to be as informed as possible when it comes to these amazing creatures.

Little Mudkip is one of my favourite lotls on this site, so I'm distressed to hear he may be distressed. But he looks great to me - no curl in that tail, gills look great. You may be worrying about nothing. Just be patient with the tank - you will get there.
As for the Prime, I have no experience with it so cannot comment on that, but I think it most unlikely that it killed the shrimp.
I do wonder whether that temperature is in fact a bit low? In lower temperatures, the metabolism can slow down so the axie may be less active.

The ammonia could have been higher because you added two more ammonia-producing animals to the tank. Now that they're gone, it might not be as much of a problem. I don't know about Prime, but I've found Stability helps ease the sharpness of ammonia spikes a bit (still not as reliable as a good ol' water change, though! It just takes the edge off).

Your temperatures don't need to be that low. 63 is heaven for axies, but the 50's might slow your little dude down and make him less active like that. As long as it isn't in the 70's you don't need to worry about actively cooling the tank. Also you should definitely share your mystical secret as to how you keep your tank at 63 without any added effort @_@ share your wisdom with us.

One thing I can think of that might cause a problem is, your axolotl doesn't quite seem big enough for shrimp just yet. Maybe it ate the two, and now is having trouble digesting the exoskeletons? Has Mudkip been passing waste regularly? Have you noticed any changes there? If you haven't noticed any droppings lately, he might be constipated. If that's the case, popping him in the fridge for a day or two could be a simple remedy. That's the only thing I can think of that might be an issue.

In the pictures you've given, Mudkip looks to be in fine shape. An important thing to remember is that axolotls are not generally a hyperactive animal. Younger ones generally swim around more, but they become a little bit more sedentary as they get older. That paired with the cooler temperatures makes me think that your axolotl is fine.

I would just monitor his droppings, keep an eye on the ammonia, do as many water changes as necessary to keep it in check, and keep an eye out for a curled tail or curled gills.

That you both for your quick responses. Since reading your posts I have started keeping my tank temps a little higher; about 63-65 Fahrenheit, and have completely cleaned all of Mudkip's decorations as well as the tank itself (using Mr.Clean magic erasers). This seemed to get her to stop hiding as much but she still seemed quite lethargic compared to how active she was in the beginning.
I think that she may have eaten the shrimp and yes they were much too big for her so that could be the cause of her discomfort. As for her droppings, it is hard to say if they were regular, I often found evidence that she has pooped, but most of the time I do not find a solid mass to remove. I assumed this was because she has been eating her droppings, but perhaps she just hadn't been going?
Another theory suggested to me was that I may be feeding a bit too much. As of now I feed Mudkip about two cubes of bloodworms every evening when previously I only fed about half a cube. I increased the amount because she eats so readily and always seems hungry, but after eating these days she definitely seems bloated and very lethargic. I'm cutting her back a bit and I think that has been helping as well.
Thank you for your advice and input, I really appreciate it.