I would very much like to do some research on the psychological methods used in U.S. Armed Services Basic Training, particularly the reasoning behind the high levels of aggression and intimidation utilized by instructors and the resulting effects on recruits. I’ve done a few hours of research on the internet, but have come up with nothing. What gives? Are Basic Training policies and procedures classified information?
Methinks you have a rather exaggerated view of Basic Trainign from watching A Certain Vietnam-War Movie with R. Lee. Ermy.
First, different branches handle differently. The marines were once a bit infamous for being a bit hardcase about it. To my knowledge, no branch fo the military uses that appraoch anymore.
Actually, I’m former U.S. Air Force. I’ve been through BMT myself. 
It’s true that Basic now is not the same it was in Full Metal Jacket. Physical contact and swearing are now prohibited. However, the drill instructors (or T.I.'s, in the USAF) do use aggression and intimidation as SOP. What is the principle behind it and what are the short- and long-term psychological effects on recruits?
Not only are Army BT standards and training manuals not classified information, but they’re readily available on the Internet. Recruits going into BT are not assigned any kind of security clearance unless they already had one upon enlistment, and nothing about BT is classified. In terms of the rationale behind BT, you probably want to look at Drill Instructor training and manuals, which explains to DIs they whats, hows, and whys of training recruits.
I’m not quite clear on what the objective is of your research, but anyone who has been through any kind of basic training–be it military, peace officer, or otherwise–is that the purpose of intimidation and harassment is to inculcate the recruit into accepting the near-absolute authority of superiors, force recruits to push themselves to physical and mental limits, and weed out recruits who are unsuitable for service through deficiency or inability to accept authority. Basic training is just that; the physical and emotional conditioning to become a well-integrated cog in a military unit, and to prepare recruits for either battlefield conditions or more specialized training. As former Army Ranger General Barry McCaffery related in a story in which he and a classmate were laying face down in a rice paddy in Viet Nam under suppressive fire, his friend looked over at him and said, “Well, at least we’re not in Ranger school.” An additional advantage is that soldiers learn to bond with each other against a common enemy; in the case of BT, against the DIs. This kind of bonding is critical when it comes to having to depend on another person to cover you arse at peril to his own delicate skin.
I don’t know if this is why what you are looking for, but Dave Grossman’s On Combat, The Psychology and Physiology of Deadly Conflict in War and in Peace and Bruce Siddle’s Sharpening the Warriors Edge: The Psychology & Science of Training go into some amount of detail between more traditionally abstract marksmanship training, and the more realistic combat training that military recruits and police officers currently undergo, which makes them more prepared for the reality of combat. In Grossman’s On Killing: The Psychological Cost of Learning to Kill in War and Society, he goes into detail on the research performed by S.L.A. Marshall follow-on studies which demonstrated that using the basic training methods employed during WWI and WWII had only about 10-15% of soldiers even discharging their weapons on the battlefield and likely even fewer actually intentionally targeting enemy soldiers, whereas using the more realistic reactive targets during training for troops sent to Viet Nam achieved >95% of soldiers discharging weapons.
It turns out to be very difficult to train most people to intentionally kill; only about 2% of the population will (with assurance that what they are doing is just and moral) pick up a weapon and kill another person without suffering significant hesitation or resulting psychological trauma, even if they are under fire or otherwise threatened. Taking raw recruits and turning them into soldiers capable of killing strangers against whom they have not personal animosity upon (and only upon) authoritative direction is very difficult; it basically entails breaking down the native resistance that 98% of people have toward killing while not turning the recruit into an uncontrollable sociopath.
Stranger
I’d also suggest Making the Corps by Thomas Ricks for a look at Marine basic training in the 90s.
You might also see if your local library has the reference set: * Military life: The psychology of serving in peace and combat*
A good article on how warriors are made, and the sometimes-unfortunate aftermath: The Price of Valor | The New Yorker