LAST
Jon,Nice to have you aboard.
First off, anything you do to practice and play the harmonica is helpful and a good thing. The caveat to this is that you want to be careful not to practice the wrong things and get into bad habits. I think overall, driving is one of the worst places to work on breathing simply because you are sitting and not standing up (at least I hope you don't drive standing). Ideally, you want to be doing "stomach breathing" and it's hard to learn correctly in a sitting position. Once you have breathing down pat, sitting or standing won't make as much of a difference.
Also, when you work on breathing, try to relax your face and shoulders, put the harmonica deep in your mouth so that you can hold it with your teeth, and breathe big chords from as low in your body as you can. Holding the harmonica with your teeth forces you to breathe and NOT just suck and blow the air from the front of your mouth.
It sounds like you are doing a lot of right things to get good. Doing the above chord drill will also help with your breathing stamina which should make playing those long held notes a bit easier. Harmonica is of course very aerobic and much of what you are experiencing now will fix itself over the next few months just by playing more and more.
Play on,
Dave