There are NO silly questions, (however silly answers.. that is another matter I'm sure
Glad to hear your fish and plants are A-OK..
I had this happen once, when the flow from the UGF was halted, and I didn't realize it, the bacteria in my UGF died, AMMONIA HECKFIRE was unleashed, lost all but 3 fish (25 died). One power head had malfunctioned on an uplift tube without me noticing it, and the impeller on my biowheel busted at the same time, (murphy's law).
Long story short, I think vigorous cleaning of the filter, in "Close" combo with the UGF removal, sent your system on reboot. The second cycle should NOT take as long as the first one you had, so don't worry so much about that, but it will take some days to get back to equilibrium.
I recommend using ONE ammonia binder or another. Ammo-lock binds more ammonia than amquel, so I would use ammo-lock. But remember, it is a BINDER, it only converts it to a less harmfull form, but it is still "ammonia" and can still be detected in test kits, AND eaten by the biological bacteria. Dose as directed.
If the ammonia is reducing,
reduce the amount of your water changes, continuing large water changes could stress out the fish if done too much, too frequently, when the system is returning to its old self.
Recommendations on feeding... Once ever other day... until your biological filter bounces back. If you are lifting out excess food with a net, you are feeding too much. Tropical fishes stomach's can be about as big as there eyes (give or take). Adult fish do not need to be fed as frequently as juvie fish (not sure if you have grown ones or not.. I'm guessing not though.)
I'm curious, what is the pH of the water you use. You'd be surprised at the pH level of some common city water systems. (Can run from Acidic to Base, just depends where you are sometimes.) If your plants and livestock are happy in that realm, you may not need to do anything drastic with the pH.
good luck with everything kiddo. Stay diligent, the natural process is well under way, and looks as if you may be coming out of the storm, so try to relax a bit, the tank is showing the beginnings of bouncing back.
nrstype