When I read your latest info, I immediately thought about pseudomonas, which is kind of like pneumonia in people (as far as I can tell), and sometimes takes a very long time to get rid of. Has that ever been mentioned. It's been coming up here on the forums lately. Here's just one thread on it:
http://www.thecatsite.com/t/261531/botans-recovery-story-pseudomonas
Now, are BOTH kitties suffering from the same issue, or just one? Also, try not to stress over this (easier said than done, I know), because your stress passes to them, as I'm sure you are aware
You've got to take care of yourself so you can take care of your new (ish) furkids.
http://www.thecatsite.com/t/261531/botans-recovery-story-pseudomonas
Now, are BOTH kitties suffering from the same issue, or just one? Also, try not to stress over this (easier said than done, I know), because your stress passes to them, as I'm sure you are aware