In manual mode I can not select the aperture but only shutter speed and exposure.

That's correct. The M42 mount doesn't have any provisions for the lens to interact with the camera in either direction, so shutter speed and sensor sensitivity (ISO) are the only things on the body you'll be able to adjust. Aperture is, obviously, on the lens.

The images turn out to be darker even at f2...

The D3100 is not listed as being able to meter with non-CPU lenses, so anything you're seeing on the meter -- if it's showing you anything at all -- should be taken with a boulder of salt. Correct exposure can be determined using an off-camera light meter or trial and error. Fortunately, trial and error is cheap on a digital body.

If the ISO sensitivity in your camera is set to automatic, it may be defaulting to 100 without proper metering input. It takes a surprising amount light at ISO 100 to get a good exposure, so do some experimentation at 400 or 800 or shoot outside in the sun.

...and out of focus.

Manual focus is difficult on most DSLRs because their focusing screens don't have anything to help you out. Before AF was common, most bodies had a split-prism or microprism focusing aid that made it clear when the image was in focus. There are third-party screens available with one or both built in. They cost just north of $100 but are worth every dime if you're going to do a lot of manual work.