R.J.
My son has mystery respiratory issues. So I'll offer up 2 things:
1) http://www.amazon.com/Concord-Fingertip-Oximeter-carrying... is a GODSEND, and I carry it around with us everywhere. If I can't get him into the 90's with his meds, we're in Children's ER (our regional children's hospital). Even if I can get him into the 90's, I chart each and every single time it drops. And omg... Yeah... my 9yo will be RUNNING around the house laughing and goofing off in the freakin' 70's (I can tell he's low, because his eyes get glassy). Most kids and adults in the 70's can't even sit up on their own. Aaaargh. Anyhow, literal lifesaver/sanity saver until you get a hospital oximeter. I'm working on getting an actual monitor for nighttime. Half the reason I'm on here so much recently is that I'm afraid to sleep. That alarm is the most relaxing sound I know. Instead I stay up until 4 or 5 in the morning most nights just to be checking on him, then sleep for a few hours.
2) Head back to Mayo. Having a child with mystery problems (and periodic hospital stays ranging from a week to a month) has REALLY highlighted the dozens and dozens of things that could be wrong from any set of symptoms. I know a family with a 2yo with similar problems as you describe, and they've been at Children's since November, after a year of hospital stays and ER trips close to where they used to live. Another family with similar problems only ever had to spend a week. Mystery problems SUCK. Granted I am SO grateful that my son has a "normal" life 50-90% of the time, but the sheer intermittentness also creates a huge problem diagnostically. ((Our own "mystery problems" could EITHER be pulmonary, neurological, or rheumatological -kiddo has a bizarre reaction to inflammation.)) Bring a list or chart of all of his spells, duration, color, all the data you possibly can bring with you.
Best of luck to you, with all my heart.