Yellow build up in my cockerels beak

Thanks for the last photos. Gives a much bigger picture.

Is this chicken lethargic? Do its eyes remain closed a lot of the time, and is it acting sick? Do you notice it having less or no appetite?

If behaving sickly, I lean toward this being canker. https://www.merckvetmanual.com/poultry/trichomonosis/trichomonosis

The lesions on the comb and wattles appear to be possible fowl pox as @Eggcessive suspects. It's possible to get hit with both. Lucky chicken.
He is lethargic. Eyes do remain closed a lot of the time, even poking its head underneath its wing and staying like that for prolonged time. Loss of appetite, not drinking water.

I hit him with a dose of ivermectin today, I have amoflox (antibiotic).

How do I continue proper treatment? Do I clean out its beak?

Thanks for the insight.
 
Double trouble.
The moisture under the wings that stinks is due to mucus discharge from the mouth of the bird that has been tucking its head under the wings. This is a sign of a very sick bird.
I highly recommend that you cull the bird and remove it away from your flock and bury it deep in the ground. Not so in as much as fowl pox, but due to the canker.
Canker is very contagious to other birds via waterers and feeders. You dont want it spreading through your flock.
 
I agree with @dawg53 that taking this rooster away from his suffering would be best for all involved. Treating him would involve removing the plaques from inside his mouth, which would be very painful, but necessary if he is to be able to eat and drink, which he cannot do now. You would need to isolate him and feed and water him by a tube into his crop.

Save yourself a lot of trouble and heartache by ending it for him. And it could prevent more chickens from coming down with this.
 
We isolated him from the rest of the flock. It seems that some other roosters have the fowl pox. Noticed some lesions on combs and wattles. Started antibiotic for that whole flock just to keep any possible infections from the lesions in check.
I will take your advice into account about the rooster that came down with canker. Earlier today while giving him water with the help of a siringe all the plaque came off when he would shake its head. But still can't find any metrodinazole here on the island. Will try some last resources tomorrow. If we see no improvement tomorrow we will sadly cull him. We were pretty surprised that apple cider is considered a good prevention method. The whole flock's water always has apple cider in it and he still came down with the canker.
 
Apple cider vinegar isnt all that it's cracked up to be, a myth. I dont use it in my birds.
Fowl pox is a virus, antibiotics are ineffective unless there's a secondary bacterial infection.
You can put iodine on the lesions to help shrink them, avoid the the eyes if you use it.
 

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