Sometimes too low of humidity can trigger RIs. It appears like you are housing him in a glass tank.  How are you heating the tank? Is it a screen top?

Do you have it partially covered?

Also, can I ask what material the hides are made out of?

Yes, I have him in a glass tank and it is a screen top, but the only thing covering it would be the heat lamp and the light hood. I have a UTH on the hot side as well as a heat lamp, but I only use the heat lamp in the winter months because I am in New England. Shouldn't the humidity be very low because he is a desert species?

His hides had been those half log ones that you commonly see, but I noticed he seemed like he was too large for them so I replaced them with some cave looking hides from a petco. I would imagine they are a form of resin.

a picture would be very helpful.

also, did your vet do a culture, or just prescribe a general broad-spectrum antibiotic? you might need a culture to be sure you have the right antibiotic for the infection he's carrying?

Desert species or not, bump up the humidity.

In the wild, when it's hot and dry, they retreat underground where its more humid. If they didn't, they'd likely get dehydrated, which is a possibility of what is happening or a contributing factor?? I would at least try to add a humid hide.

Thank you for all of the responses! It's so awesome to see that there is a community like this.

Aimee, I have posted a photo of his entire enclosure. As you can see, I have  aspen, a water dish and 3 hides as well as some decor. Hot side is 92 and cool side goes between 72-75.

I wouldn't want to bumb up the humidity for the entire tank, but I could add more aspen so he can burrow more and make one of the hides a humid hide. 

I am going to the vet tomorrow so I will add to this post tomorrow.

Please do...

So I went to the vet today and there is quite a conundrum. Fortunately, I have a great vet who is a reptile specialist so he really knows his stuff. Apparently, he does not have a respitory issue, but has lost 10% of his body mass. He ran an xray and nothing abnormal came up so he decided to draw blood. As soon as he held him vertically to draw blood he began signifigantly bleeding from his cloaca. Not only was there blood, but some pus as well. He now believes it is a bacterial infection or a parasite so he has given an anti worming medication and anti-biotics over the next few days. He said my enviorment is fine and most likely this is something that he had when I puchased him and it is only now surfacing.

Since Balboa was obviously very stressed from everything we are going to wait a few days before we go in and try drawing blood again. 

Oh no, that doesn't sound good. I wonder if shipping/the transfer to his new home was enough of a stressor to trigger a parasite or whatever it is that had been sitting dormant in him. 

Please continue to update us as you learn anything. It helps us all learn.

Thank you for this update.