I had somehow accidentally submitted my application online in mid July. I was given the same notice, with my respective portions missing. (PFT, Interview, Transcripts, Statement) If you read carefully, it says to respond within 15 days of receiving your letter. You have a phone number for your Point of Contact regarding the scholarship. Use it.
After this letter, my PFT was done the next day. I had all my paperwork complete by the next time I could enter the school (two days later) and faxed it all in. And my school's computer system was down, with no access to transcripts or anything. Yet I was still able to get a copy from the wonderful ladies who work at guidance. Politeness and professionalism can go very far. My interview was later that same day. My application was officially complete the next week after.
The CFA scores from USMA will not count for the PFT. They are two different tests. The PFT is actually easier.
As for being DQ'd, I cannot say. I took no chances, and had all my application in within 3 days of my letter. How I submitted mine online, not fully complete, is beyond me. I don't recall ever laying eyes on the final online submission page. But that's not important. What's important is that somewhere, something went awry, and the mistake was promptly corrected. And my school doesn't begin for another 10 days. This happened to me in mid-July.
Get it all done. It is possible, so long as you put your mind to it! =]