There's a dot on my pictures & I have cleaned the mirrors inside the D40x. I'm sure that it's coming from the body not the lens. What can cause this?

check to see that mirror goes all the way up

check to make sure secondary mirror attached to bottom of main mirror goes all the way up when mirror goes up

check to make sure a shutter blade is out of place or broken

for all of these set the camera on manual and bulb, and set it to fire without a card, and then take off the lens and look in the mirror box when firing

Lens motor(inside the lens) could be damaged already. The D40x focusing system is dependent on the lens, just like any other Nikon Dx camera except for the ones that has built-in motor to its body, e.g. D90, D7000. Try a different lens, most likely it should work

Hiit is simple dust particles. I can let you know by very simple tip. But unfortunately I can not describe in word everything. First thing you can try is that you can you ear know remover or squeeze blower. Set the camera at ccd cleaning mode.(not auto mode) See front inside of mirror box when mirror goes up, you can recognize the brown spot. Blow with the blower. Other method is I can not expain everything.

Clean the contacts on the body and the lens where they meet with a cotton swab lightly dampened in rubbing alcohol. See if that makes a difference.

Please...do not touch the mirror!!! The black dot is dust on the sensor. Google the words...digital camera sensor cleaning. You will get complete directions and where to buy the supplies.

If Alex's comment didn't resolve your problem, check for dust inside the camera body and on the part of the lens that goes into the camera body. The highlight indicator he speaks of will show on the LCD screen, but should not show up on your final picture once downloaded from the camera. Since the optics on that end of the lens are smaller, they are more susceptible to dust and dirt. If there is dirt or dust inside the camera body and you are not familiar with how to clean it, same yourself some headaches and take it to a qualified camera shop. You can seriously damage the interior optics of your camera by attempting to clean it the wrong way.

Have you cleaned to sensor on the camera? The sensor is located behind the mirror. Be very careful . Read your manual on how to do this. Most camera store will clean the sensor for you for a price. You can do this on your own but be careful not to scratch the sensor.

It seems that the lens is restricting the operation of the camera mechanism a possible cause may be the lens actuating mechanism is stiff from being underused, from you description the manual setting for your lens is ok but when attached to the camera the pin on the lens which is activated by a bar situated in the camera at the bottom of the lens mount cannot be pushed fully home. Try pushing the pin on the end of the lens to see if it is being restricted and if so may need cleaning or just a few operations to free it off.
SUPER8

Usually tele lenses need longer exposure,and mirror lenses need more than normal lenses.Try with 1sec, half sec,( 2 in the speed dial, not 2" ) or quarter sec (4 in the speed dial) exposures.

One more thing, you need good sturdy stands to hold cameras.

take the lens out and blow air inside the camera and on the inside part of the lens.