Great– always wonderful when a solution is straightforward. :)
On the pen issue:
The first question is, “Is the pen lift motor working?” That is to say, when you toggle the pen position up and down in the Setup tab, does the pen lift motor move?
Assuming that it does, you then need to adjust the two percentage values there, such that (1) the pen arm is roughly horizontal, or very slightly below, when “down” and (2) The pen arm is very slightly above horizontal when in the “up” position.
After that, put the EggBot in the “pen up” position, and insert the pen, so that it is just above — not touching — the egg (or other object that you are printing upon). You may need to adjust the vertical position of the upper pen arm in order to get it high or low enough for this.