I am/was in the same situation as you... Now I'm just waiting to attend orientation on Monday. What host school (if not your own school's campus) are you trying to attend for AROTC? First thing you should do is contact the PMS at the school, or the enrollment officer/ROO. They should be able to guide you through the whole thing. It also depends whether you're contracting right now or not. I'm guessing you're simply enrolling in either MSI or MSII right now. You don't need to fill out any of the application materials for contracting cadets if you're simply enrolling, at least for now. By the end of the year, when you're done with the basic course, is probably when you contract (most certainly before you go on the advanced course, that's for sure). I don't know the exact materials for when you contract (as I am not doing so myself right now) but I would guess it consists of a full DoDMERB physical, a copy of your transcript, a passing APFT score, and a few other things, among them the 104R.
However, if you're simply enrolling, as I just did, then it's much simpler and it requires much fewer paperwork/materials... Although I'm sure it varies by school. When I contacted the ROO at the host school, he simply had me fill out the first 2 pages of the 139-R, e-mail it back to him, and then wait to attend orientation, a diagnostic PT exam, and the actual lab/lecture/PT sessions. I also had to fill out a uniform size sheet, although this sheet is not from Cadet Command and came straight from the host school.
Here's a link to the 139-R. I'm assuming your school uses it too, but the enrollment officer at your school is the only one that can give you the most up-to-date info.
http://www.wpi.edu/Images/CMS/MilSci/CC_Form_139R_-_Cadet_Enrollment_Reocrd.xls
The 104-R form... I myself did not have to fill this out, so I'm assuming it's used when you're contracting, but here's the link anyway:
www.armyrotc.gatech.edu/Cadet Resources/Forms/ccf104r.xls
Good luck.
EDIT:
By the way, I didn't even have to provide proof of citizenship, a copy of my social security card, or other ID materials for when I was enrolling. They replied back that I'd only need them when/if I contract. Hope that helps. Keep in mind, this is bound to vary by school. Good luck.