Okay so an update.
As stated before i tested my tap water and there were and still are trace amounts of ammonia. On a whim i pulled out our drinking water from the fridge, a Brita filter pitcher. Poured a small glass and tested it. NO ammonia was detected in this water. I also tested PH and GH and everything seemed to be okay. The ph was a little lower than my tank but i figured the ammonia being at zero was a bigger benefit that the ph levels being harmful. I did a 40-50% water change with the filtered water. (not straight from the fridge, that would be too cold) Ammonia levels were cut in half within an hour. From the 2ppm to 1ppm. So i think i have figured out my source for water changes. Very inconvenient but worth it for the fish.
Now that i am slowly getting the finishing stages of the cycle under control, i am still worried about his eating habits. Again, as i stated, he will not eat now. He gets scared and hides when i go to feed him now that he has the hiding spots. I think adding more fish will help him in the end but i do not want to add more fish to the cycling aquarium. If i would have done my research before setting it up and buying i would have no fish in there but here i am now. I tried covering the sides so he couldn't see me and drop food in when he is out and about, nothing. I tried putting the flakes in a syringe and squirting it to his hideout, just a nibble. In the last 5 days he has only eaten one small piece of food and i am getting worried it will not be good for him soon.
Any other suggestions?