Did the vet say how he knew the chameleon had an infection?
If the medication doesn't seem to be causing some improvement
by the time you've been giving it to him for a few days
(and its been a few days now), then I would suggest that
you talk to the vet about it. Its possible that the
baytril doesn't work on whatever is causing the infection.
With mouth rot or a wound its easy to get a swab/sample of
the pus. The bacteria could be grown and a test done to see
which antibiotic would kill that germ....but with a respiratory
problem its a different story. Its harder to get a bacteria
sample.
The fact that he isn't drinking on his own worries me. As someone
already mentioned, you need to keep him well hydrated while he's
on the medications. I can understand that he might not be feeling
like eating...but that can't go on for too long. If the
antibiotic was working, I would think he would begin to feel
more like eating.
What I have done when a chameleon doesn't eat on its own is,
while his mouth is open while he's drinking, slip a cricket that
is not too big in between his teeth. (I usually squish/kill the
cricket so that it will not bite or climb back out of the mouth.)
He may eat it this way. This is less stressful than forcefeeding would be
and if he won't eat it this way he won't likely eat it if he's
forcefed.
You said he had a fecal done....did it turn up anything? Is that
why he's on the second antibiotic?
Is his movement around the cage normal once he has opened
his eyes or is it more like he's in a bit of a stupor? (Wandering
aimlessly?)
You said you have a humidifier going...is it kept clean? Does it
shut off in time to let his cage dry out for the night? His cage
isn't near a window or in a draft, is it?
I don't know what the flakey thing you saw on the eye could have
been (unless it was a piece of shed). What are the eyedrops you
are using?
It might be a good idea to bump the temperature of the basking
area up to 85F or so.
With him being on three different medications, this might be why
he's sleeping more/longer...or there could be other reasons.
I have used baytril quite a few times on different chameleons
with different problems over the years with good results. I can't
remember the dosage (the weight of each chameleon was different
so the dose was different for each one)...but it was given orally
every day. Three weeks has often been the time frame for giving
it to them.
Good luck with him!