So i took foggycreekcavy's advice and broke up my post to make it easier for everyone to read. Thank you in advance for any advice!!
So another update...
Both boys have been on the Doxy for eleven days now. I didn't really see any improvement over the first week but am giving another week now because they have been on so many different A/Bs already and i don't want to hop around without giving it a chance. They don't seem to be getting worse, which is good, but don't seem to be improving either.
Turbo still has some labored breathing going on, sometimes he sounds good, sometimes he doesn't. He's still sneezing, although less i believe, with snot coming out upon sneezing. Diesel still has a bit of crusty nose and some snot upon sneezing. I am running a vaporizer plenty during the day to give them more moisture as the vet advised, but not too close because i worry about making it cold for them.
Turbo-three weeks of Baytril, two weeks of Bactrim, now eleven days of Doxy. Diesel-two weeks of Bactrim for possible UTI, then he started this sneezing and snot thing at the end of the Bactrim and is doing the Doxy the same as Turbo.
So my question is, what do i do next? I'm still holding out hope that the Doxy will kick it, they both have the 5mg/kg dose Pinta recommends on GL. How long should i stick with the Doxy before i try something different, and what do i do next? Neubulizer, Baytril/Doxy combo, higher Baytril dose alone?? Diesel won't tolerate Baytril, so maybe a Bactrim/Doxy combo??
The good news is that everyone is eating and drinking fine, maintaining their weight (they get weighed twice a day before meds). I feel like they are not as active as they should be, they hide most of the day in their hideys, whether in their cage or in the floor time enclosure, both of which are very big. They both also have a bit of fungal ear, Diesel more than Turbo, which i was treating with Lamisil, but now am treating with Monistat to see if i get more improvement.
Whew, sorry for the long post, just get it all out now, huh?

I have seen them be a little more vocal the last few days and was hoping that was a good sign.