When i turn the camera on, the F (aperature) button blinks, not allowing the camera to focus, even in auto mode. when this happens, i can't even customize my setting on A or S priority. I am frustrated because i can't get my camera to take a picture until the camera decides to focus itself!

Please check if yu did set the camera in AF mode continuous. In that mode, the camera is focusing on whatever is aimed at. Even when the shutter button is not pressed, allowing you to shoot without missing opportunities.
The mode where you see the camera focus when the button is pressed half way, is called single. This setting will conserve battery power.
Look in the manual under Switching between Focus Settings. I can't tell you war page that is for your camera, in mine it is page 100.
On the last pages in the book are all settings for each shooting mode.

Are you using an auto-focus m4/3 lens? I have about 20 lenses for this camera and only 1 of them is an auto-focus m4/3 lens. I have an adapter so I can use my 4/3 lenses on it in auto-focus mode along with other various mounts (including cctv) that do not support auto-focus. So if you are using a non-auto-focus lens, you will need to manually focus the pictures.
If you are certain it is an auto-focus lens, are you sure you have it set to auto-focus?
What settings do you have your camera set to (aperature mostly is what I'd like to know)? Try adjusting your aperature to be small (to increase your DOF).
Also what lens are you using and what is your focal distance? It could be your lens has a larger or shallower focal distance than what you are trying to achieve (like a macro lens doesn't work that great for landscape photography or a telephoto lens doesn't work great for macro photography).
Last thought: is your lens or sensor dirty? A dirty lens can cause focusing issues if it is REALLY dirty and a dirty sensor can too (sensor is a bigger pain to clean. I strongly recommend taking it to the pros as they scratch really easily). Dirty lenses can be cleaned with a blower and a lint free cloth and rubbing alcohol if those 2 things don't clear it out.

The D90 has three different autofocus modes. In the AF-S mode it will not shoot until it has focused. In the AF-C mode it will shoot when you press the shutter release button even if has not focused. In the AF-A mode the camera switches between the AF-S and AF-C modes so either can apply.Also, bear in mind that the camera doesn't really know what you're taking a picture of. It may focus on something other than your subject. If you're in the single-area AF mode then you control which of the eleven focus points the camera uses. In any of the dynamic-area AF modes the camera decides.For full details on how the various modes work, please consult your manual. You might also check out the Nikon D90 video tutorial.

Are you using the 50mm lens with aperture ring, if so move to th largest F no and try again.

Send it back ASAP to get the problem corrected in warranty also see if Ritz or another camera store can figure it out before you send it off. Consider getting a warranty from Squaretrade.com within 90 days of your purchase I hope this helps. They also have accidental damage protection too for a reasonable rate.

excuse me if this is a dumb question but you wouldn't believe the things people do...., but in manual mode are you actually manually trying to move the lens? as manual mode means just that you take hold of the lens and turn it. If it wont turn it sounds like the lens is jammed and needs returning/repairing.

if taking hold of the lens and turning it works for manual mode, take the lens off and clean the gold contacts on both the camera and the lens with a pencil erasor this may bring the auto focus back to life, switch back to auto and try again, if not its most likely the lens but take the body to a canon store and try another lens just to double check the body is ok

drop me a line if i can be of further assistance

best of luck

My flash doesnt work either. Holding the flash button down doesnt do anything either (in program mode)

Things to check before you assume it is a mechanical issue-you can get vibration message if flash is disabled, be sure also that the macro mode is not enabled-this is very common on sony cameras to turn on by accident-flower button on camera will put in close up mode and you will get blur make sure no flower is present on lcd screen-if in macro press button on camera w/flower to turn off-also in menu you have continuous and monitor auto focus settings try changing one or the other and see what happens

There are four focus modes: S-AF (Single auto focus), C-AF (Continuous auto focus), MF (Manual Focus), and S-AF/MF (Simultaneous mode). (SINGLE Auto Focus): Focusing is performed once when the shutter button is pressed halfway. C-AF (CONTINUOUS Auto Focus): The camera repeats focusing while the shutter button is pressed halfway. (MANUAL FOCUS): The function allows you to manually focus on any subject while looking through the viewfinder. SIMULTANEOUS USE of S-AF mode and MF mode: You can fine-adjust focus manually by turning the focus ring after AF is performed in the S-AF mode.

The cause and solution may include one of the following: The camera is not turned on. Turn on the camera. The camera is processing a picture; the camera Power ring light (on the Mode dial) blinks green. Wait until the light stops blinking before taking another picture. The card or internal memory is full. Transfer pictures to the computer, delete pictures from the camera, switch storage locations, or insert a memory card with available memory. The shutter button was not pressed. Depress the shutter button completely down. There was a failure in the focus and/or exposure. Press the shutter button halfway to set the Auto Focus (AF) and Auto Exposure (AE). When the AF/AE indicator turns green, press the shutter button completely down. The battery is exhausted. Replace or recharge the battery