Thanks, by experimenting I have discovered all those things. The misalignment was partly the line being oriented the wrong way and partly a weird offset in the body of the part, it seems that the bendable lead also wants to be in the center of the body of the part in order to be correct on the grid. As well there is a strange interaction in Inkscape on the line. If I reduce the height of the line (the direction opposite to stroke width) from the 50 it was down to 30 so the line is circular (after I figured out I needed to be inheriting the stroke-cap round as well) I have to set it to 20 multiple times and it moves vertically (and reduces the height by perhaps 10 each iteration) until I can get it down to the 30 that I want. I don't know why but in the end I got it where I want it and it now seems to be working correctly. So this version should do what the OP wanted with all 3 issues fixed:
2wire_pb_bendable_legs.fzpz (6.6 KB)
Peter