1) You don't send letters directly to AACOMAS except through Interfolio. If you use interfolio and pay the proper fees, I don't see why it wouldn't be.
2) You can apply without having all the prereqs done. If accepted, it will likely be conditional upon completion.
3) Most schools ask for specific recommendations. Anything beyond this is worthless and will be thrown away (as I have been told by a couple schools). And getting a letter from a PA is awesome if you are applying for PA school. If not, worthless. You need to have a letter from a physician and if you are applying to any of the schools that require DO letters, it needs do be from a DO. A volunteer letter is worthless too.