Nice job on the pens, both of you. I think the second one is padauk also.
For the pictures, I'm guessing you are using a white or nearly so background. I'm also guessing you are using auto exposure mode. Your camera is designed, when in auto mode, to average the exposure so that, overall, the picture (in black and white terms) is a shade of gray. With all the white and not much brown, it is net letting the correct amount of light in, thus giving you an overall dark exposure. I think you also need a tripod to hold the camera steady.
It would help to keep the pen parallel to the camera lens, which will let you keep the whole pen in focus at once. If you know how to shoot in manual or aperture priority mode, set your aperture (f-stop) at about 8, and use a very slow shutter speed to let a little more light in. The smaller (physical size, not number) aperture will give you more depth of field, which means that a greater area will be in focus. The low shutter speed will make a tripod necessary.
The folks in the photography forum here are very helpful, and can help get you up to speed in that department.
Dan