Also, Baytril may not be effective against the pathogen, if it is even infectious. Obstructions of the respiratory tract may also cause RI-like symptoms, and can range from a foreign body to a growth.
If it is a bacterial infection, the dose of Baytril (enrofloxacin) you are giving may not be accurate (especially with oral meds in such a small animal) or effective.
Enrofloxacin, even in reptiles, is typically given once a day or every other day to obtain a therapeutic level in the animal's body. The bacterial pathogen may not even be susecptible to enrofloxacin, which does occur.
If the pathogen is a fungus or virus, then enrofloxacin, which is antibacterial, will also not be effective.
I agree with Lizarman on the heat mat issue... Sceloporus sp. are diurnal heliotherms- They require an overhead heat source so that they may bask. While a heat mat is increasing the ambient temperature of the enclosure, it is not the natural way that this species would seek out heat. Also remember to check your temps so that it doesn't get too hot. I am not familiar with the preferred temperature range of these lizards (and it probably varies with different species of fence lizard), but make sure he has the high end of the temperature range available as well as a place to cool down if he chooses.
A vet visit would be his best chance!
Good luck, and keep us posted 
Christina
www.herptiles.net