Piercet,
Thanks for the guide. It was very useful. With a little help from the Reprap IRC (I didn’t know how to access the steps with the Arduino but they showed me how to do with the G-code,) I was able to update my steps. If my measurements were correct I was off 5 steps but I didn’t have time to do a test print. 
Where do I do the drop in nuts? How do I do that? Do I need to pause? 
I don’t need to generate support material, right? Based on the STL I saw it looks like it has support material already built in. I was just concerned about some of the gaps for the nuts.
Sorry for all the questions, I am just trying to baby the extruder along and don’t want to have to print several of them via trial and error. 
With regards to 3D printing, I understand what Albert Einstien meant when he said:
“The more I learn, the more I realize how much I don’t know.”
I would like to do some of your upgrades once I figure out how to get what I have working well and some what reliably. I have all the parts for the 60mm height increase printed and on my desk. 