Yeah, your advisor normally asks for your board score reports so they already have them uploaded. I'm guessing they already have your Step 1/Level 1 scores if you are a rising 4th year. But yes, email is how that is done, as well. As for LORs, I think there was a maximum of 3 or 4.
I found a few of the documents they emailed out last year. Around June, Patricia Norman sends out an email with the Letter of Information (LOI) with all the general instructions for applying. It might say to use MODS, but that's just the army not updating documents, per usual.