I thought no one was answering because they'd be telling you what you don't want to hear, which is that most likely there's a VERY low chance that you'll now get your number one choice without a nomination there. There is only one VP nom per school per year (approximately), plus that and the supe's noms are far more likely to be used for someone who had an LOA and was unable to get a nom from their MOC, than for someone who didn't ask for that nom in the first place (at least as a first choice).
My son has a friend in a very similar situation (LOA's to his #2 & 3 schools), but he did what I think was a "smarter" thing and asked for noms from the two options (his senators won't duplicate) for his #1 and 2 schools. So now he has the sure thing (appointment since he got the nom) to his number 2, but at least has a nom to #1 to give him a chance on the slate/wait list, or wherever.
I don't know where you are (or how competitive it is), but in some places it might be possible to call whoever you got the #3 nom from and ask about switching it to your #1 school. Without the nom, I really don't think you have a chance. Either way, you'd still have your backup, which is all you have right now really. I do realize that in many states/districts this would not be possible. We're not in a competitive area, and while I know my son couldn't call his senators, I'd bet if he called his congressman's office and asked them to put him on his #3 choice, it wouldn't be a problem (he only asked for 2).
Sorry to be negative, but that's the way I see it from following these boards for a year! Definitely not an expert though, so hopefully it could work out for you and I wish you the best of luck!