I will refer you to the email you likely received inviting you to reapply, which says that any letters you may have may be presented in person if you're called for an interview because you won't be able to upload them during the application process this time.

To answer your other question, I did paste in my cover letter above my resume in the text box. But as I and others have pointed out, those things don't seem to be the deciding factor in who gets an interview. It seems to require face time in one forum or another.