Here was what happened...
Come home from college, the fish is in my parents' care (They take care of a 75 gallon Parrot tank and my 55 Gallon FH tank when I'm gone).
Oh, and my tank is fully cycled, it's been going for about a year and a half.
Unfortunately, I have no idea what happened, but the water parameters were all messed up when I get back. Ammonia was at 3.0 ppm, PH had dropped to about 5.6, and there was some Nitrite/Nitrate in the water.
My Flowerhorn got HITH, which caused a pretty big crater (that is now healing thankfully), and Popeye.
I did a 20% water change, and then immediately used Ammonia Clear (some sort of tablet) to get rid of the ammonia. After that, I have been water changing every day, and I have been using an Epsom Salt treatment to relieve his eyes (fluid build up, slightly cloudy). He is slowly getting better, his color is back (he was pale before) and his eyes are starting to recover. The hole is getting much smaller then it once was also, and the smaller ones along the lateral lines are closing up also.
I also rinsed out the filter, as it's been a long time since I changed that.
So far he is moving around, and he seems to be able to keep track of people moving around the tank. He hasn't eaten since getting sick, but since he is improving I think he will eat eventually. With the stable water conditions now (I have 7.3 PH, I turned the Temp up a little, and Ammonia levels are down to .25, no Nitrite/Nitrate), I plan on water changing about once a week now, while monitoring the water every day.
Anyways, should I use any medications? I just want to cover all my bases and ensure my Flowerhorn is well on it's way to recovery. Next time, I'm not going to leave my fish in the care of my parents. Only in a three week period my Flowerhorn nearly died because of them. I think what happened was that the buffer crashed on me, and so the PH dropped, and Ammonia levels spiked up. The fact that they only feed him Krill doesn't help (when I tell them they have to feed him pellets and other types of foods also, even if he doesn't want to eat it).