<p>I have adjusted my z axis end stop via the paper test. However when I press to home all the axis the z axis hits the print bed moves it down slightly then goes to the postion I describe. Is this how its supose to be if not what do I need to do?</p>

According to the RepRap.org
list of G-Code commands
, see
G0 & G1: Move
:
The
```
Ennn
```
command is
The amount to extrude between the starting point and ending point
.
However, according to
this
a discussion, that is now deleted from GitHub, about the Cura slicing engine:
The
E
values are in
absolute mode
, so perhaps the firmware is attempting to move the stepper motor to the absolute position (which is almost 50% through your print). This may lead to clogging or skipping depending on how hot your extruder is at that point.
As a last resort, you can perform a Boolean subtract on your model of the section that's already printed and re-slice the model to print the remaining bit. Then glue, or ABS weld, the remaining piece to the main print. I've done this in the past, it's not super glamorous, but it gets the job done if the part doesn't require a lot of structural integrity.
I was incorrect with the following statements with regard to the Cura slicing engine:
It's been a while since I've looked at 3D printer G-Code, but from what I remember,
E
values can be the bane of any manually written G-Code. Usually the slicing engine generates the
E
value as an incremental step value throughout the G-Code (at least this was true for Skeinforge and early MakerWare, please verify this). So, if the value is incremental and depending on the controller, this value could be lost or corrupt if a new print is initialized.
I would hope, that if you're using a slicing engine's
custom G-Code
input, that the software would be able to compensate situations like this and reformat your provided G-Code to match the value of
E
or any similar command.