Can't determine if this is a fraudulent email or not...

Never ascribe to malice that which can be explained through incompetence. I mean, really. Do you think there is an active e-mail scamming business built around asking people to complete their applications for CIA jobs? Really? And they happen to have an @ucia.gov e-mail address for receiving the scam replies? I've gotten lots of fake Paypal e-mails, and lots of fake Fedex e-mails, and lots of fake e-fax e-mails. I've never gotten a fake e-mail purporting to be from the CIA asking me to provide additional application materials. I don't know anyone else who has ever gotten one of those, either. Sure, be careful about what you provide in clear text via e-mail. Sure, follow up by phone on Monday. But don't spend time worrying about whether or not this is a scam.

I doubt very highly that they would be playing spycraft mindgames in this kind of communication. If they ARE doing that and it is making you crazy, maybe you aren't a good fit for that organization? But again, the vast majority of what they do is just plain old federal employment where they aren't going to play games. The shadowy, secretive stuff is mostly a Hollywood creation. The clandestine service side isn't just going to pick out some college student and toy with them. If the headers of the email match what you expect, I doubt it's fraudulent. Just written by some intern in the HR department. On the other hand, I completely agree with your list of concerns. You can't be expected to get your school to produce a transcript over a weekend, and they can't expect everyone to be cool with sending their social security number in an unencrypted email. Call the program office Monday. Better safe than sorry. If they are going to penalize you for not meeting these somewhat ridiculous requirements, it's probably not going to be a good program.

I once applied for the CIA clandestine service (and decided mid-way I didn't want to join, also I think I'm probably ineligible anyway for other reasons) and the application process was pretty old school. I got e-mailed back by a recruiter for a phone interview, and after I passed that I had to do a little online IQ test, and then they sent me a document package by regular post to fill out. They asked for me to mail back my transcripts and the supplemental form sounded pretty similar to what you describe (what were your favorite courses, where have you traveled, etc). But this was several years ago so by now it's totally possible they handle all the document sending electronically. Everything was very straightforward; unless there was some crazy meta shit going on I never once suspected I was being "tested" beyond the very ordinary questions they asked me in the phone screening, IQ test, and supplemental forms. If you're just applying for a scholarship honestly it's not like they're going to play secret agent mind games with you, this isn't some Jason Bourne shit. There are tons of people who apply for actual jobs with them; they don't have the time or resources to do secret agent tests with every single college kid who applies for a scholarship. At the end of the day you have to remember they're just another US government organization and the way they do things can be kind of slow and bureaucratic like any other US government agency. If you want the scholarship I'd go ahead and just reply back with what they want in the time frame they asked for.

The people who would be sending paperwork for this kind of thing are pretty likely to be entry level employees themselves.

Also I sincerely doubt "I question the veracity of this email because typos" will go over well.

Answer the questions and send an unofficial transcript, but withhold your SSN for now. In the body of the email just write something like "I have questions about how the SSN is used. I plan to call Monday morning to clarify but am sending the rest of the application materials now." They're unlikely to ding you if you send everything else in on time and being worried about giving out your SSN is common enough these days that it won't seem weird. I wouldn't say anything about thinking that it's a scam.

Ucia. Gov is a real cia domain for communicating with the outside world.

For comparison: A few years I was going through my e-mail on my iPhone while walking down the sidewalk, deleting items based on the subject lines. I saw an e-mail with an unpronounceable asian-looking return address with a subject line in all caps IMPORTANT BUSINESS OPPORTUNITY. Spam, right? So I deleted it. But half a second later I had second thoughts. I navigated to the trash folder, found the e-mail, and moved it back to my in-box. When I looked at the contents, it turned out to be from someone in the marketing department of the Apple App Store, asking if my iOS app company wanted to participate in an App Store promotion. Needless to say I was thrilled, I replied, and it was a good thing. The moral: even very large competent organizations send out e-mail that looks like spam.

It's probably legit. Send unofficial copies if your transcripts using the school's registrar's page, and keep it moving.