coltrane,
Not all schools require a DO letter. I believe that all schools require a letter from a physician, and they prefer a DO, but will accept an MD letter.
I may be strung up and shot at for recommending this, but for the schools you applied to that don't specify a DO letter (i.e.-will accept a letter from an MD), I would go ahead and send the MD letter, and get your files completed now. If your MD letter is as good as you say and you've worked with this doc for a while, it will probably portray you and your abilities more positively than a letter from a DO who you only shadow for one day--and at this point in the app game, you won't have a lot of time to shadow/get to know this DO before you need the letter.
Obviously, for the schools that require the DO letter, continue with your shadowing plans and get that letter. Another option, some schools allow you to send more letters than they require. If this is the case at any of the schools you applied to, then send both. Your MD letter will describe you positively and describe your work ethic and ability, and your DO letter will show that you've made an effort to investigate the differences between MD/DO, and made the effort to observe a DO in action.
Good luck.