Hi mell.
Yeah, I suppose that is confusing. "Ammonia" comes in two forms. 1 - 'Free ammonia' which is chemically NH3, and is the highly toxic form. 2 - 'Ammonium' which is chemically an ion NH4, this isn't as big a concern for the fish.
Ammonia & ammonium will be present in the tank whenever you have the fish... they release it through respiration through their gills constantly. There is a set ratio for how much is in each form, and the ratio is set by the salinity (nil in your case), temperature and pH. The lower the pH the more ammonium and the less ammonia... so its a safer way for the cycle to proceed. The higher the pH the more ammonia and it becomes more dangerous to the fish... of course, the interesting part is that the bacteria generally reproduce better at those higher pHs, and less so at the lower pHs.
Anyway, there is a calculator you can use to determine what your value for free ammonia actually is, as you test kit actually tests for BOTH forms, not one or the other.
http/www.hamzasreef.com/Contents/Calculators/FreeAmmonia.php
You can use this link to see where the toxicity levels are for your fish, in general.
http/www.thekrib.com/Chemistry/ammonia-toxicity.html
Ultimately, the levels you have and the temp, your fish are 'safe' at the ammonia level you are reading, with your pH and temp.
The problems are the levels from before have taken their toll... But, I don't believe you are still getting a true ammonia reading. Be sure to take your reading in natural light.
Let the tank sit for two days and test. If you get the same reading, then its likely it is just how you are interpreting the color. Then, begin to monitor for nitrite, as that is the next big concern.