Welcome to the ortho application circus.
Most schools will accept everything piecemeal and have a secretary devoted to putting everything together in your file. Once your file is complete, they'll put it aside with the other complete files to go on to the admissions committee once they're ready for it (usually after the program's application deadline).
Catfish - just order a bunch of transcripts sent to you, and you can send them along with other items the school might require (photos, separate CV, etc.). I included a cover letter with the transcripts in a manilla envelope, indicating my name and that I was applying to orthodontics, and itemizing what I included in the envelope. This way they'll know to file it away and where it'll go, especially since some schools may have you send your stuff to a general "advanced education" department. Also, none of the schools I applied to had any problem receiving the transcript from me so long as it was stamped or signed along the seal of the envelope.
The board scores are a huge hassle, I agree, and the form doesn't even give you enough room to write the mailing addresses clearly in one box. Astounding. I just printed out a separate sheet with all the addresses and wrote in one of the boxes on their form "see attached forms" and stapled everything together. I did 10 at once and it wasn't a problem. Also, many schools will accept the scores in your dean's letter as official scores, even some of those that indicate that they require official score reports.
