Not sure what you mean by focal length of 42 and 29. Zoom lens settings? BTW, what camera are you using? Full frame or APS-C, or?? That matters in assessing your focal length. You want to get as far away as you can but still fill the frame and accomplishing that will depend on your lens focal length(s). That's why a lot of folks use a long (100mm) macro. Also, the further you are away from the subject the greater your depth of field will be. At the same time, you can lose ultimate detail because you may be too far away. Lots of trades to make!
Do you know what 18% gray is? It is a great starting point for adjusting your final color temperature. On my screen (which is calibrated) your picture looks still a bit warm but maybe that's how you like it. Typically, what I'll do is use the software color balance adjustments to make the light box background look roughly 18% gray and then go from there. If you know how to look at the RGB values for your background then that will help and those values will vary depending on gamma and color space (I now you wanted this simple!) but they're around R120, G120, B120.
Focus is critical. I have found that manual focusing is best for me because the camera sometimes wants to focus on something other than what is important. BSea says likewise. I think your latest profile shot is good and one thing I would do in addition is just rotate the pen so more of the clip can be seen. The other thing I'd do is use a different stand, or something, so that the tip isn't hidden. You could still use the same stand but just offset the tip/nose cone so that it doesn't go in the hole.
What software are you using?
Cheers,
Rich