Sorry to hear... I also deal with long term management of old injuries and it's frustrating. Anyway, there are a couple of "breath trainers" on the market. I have no idea if they actually would help with your situation.
http://www.powerbreathe.com/
Otherwise, yeah, fitness will help.
In general I'd say, get on the trainer (for safety) and do the kind of intervals that cause you the most difficulty.