A water change shouldn't do any harm unless the new water was drastically different from the old water...big temperature difference, big pH difference, etc. Or you've gone a very long time since your last water change. From what I've been told having a pH that is too high or low isn't a big deal unless you are trying to breed a difficult to breed fish. If not, all that matters is that it's always the same. Sometimes trying to make it perfect does more harm than good, consistency is better.
There shouldn't have been a temp difference because I took the fish out and put him in a vase. I added new water to the tank and turned the heater off. left the fish in the vase overnight and put him back in the tank in the morning. Then I turned the heater on with the fish already in the tank so he could warm up gradually.
Does your water conditioner remove both chlorine and chloramines? What about heavy metals?
Yes, yes, and yes.
Having ammonia in the water is a problem, how often have you been changing the water? Are you using a liquid test kit or strips? Does it test nitrite or nitrate? Does the tank have a filter? If there is no filter then it's possible you accidentally caused the tank to start re-cycling by eliminating too much of the nitrogen fixing bacteria in the water/in the gravel (if you use a gravel vacuum). In that case you'll need to get a filter, or at least filter media for bacteria to grow on and then do frequent water change until the tank has cycled (bacteria has grown). Testing for nitrites and nitrates will tell us if this is what has happened.
Liquid test kit (just bought it). It doesn't test nitrates. They had a big one that did multiple things, but I'm on a grad school budget and so I only got the ammonia and pH (those things are pricy)! Yes and no on the filter. Yes, I have one, but I didn't put it in until this water change, so I'm pretty sure I destroyed my population of good bacteria. I've only been turning it on for a little bit per day because the water flow is a bit strong for my little fish.
I don't think I cleaned my tank the right way. I put the fish in a vase, took out a few gallons of water off the top and kept it in buckets and then dumped the rest of the tank down the drain. Washed out all of the gravel and decorations and then put the old water that I'd saved back in. I then added tap water to refill the remaining empty tank space and added some stress coat to decontaminate the tap water. I waited overnight and then re-added the fish to the tank. It was probably more of an overhaul than I should have done.
I've only had the fish 2.5 months, but I've done a big clean like this twice now (about once per month). In the in-between times, I've been taking out out a gallon or so once every week or two and replacing it with pre-dechlorinated water. The fish seemed to handle the first big tank cleaning okay, but the second one less so.