I actually deleted the .ini files from that repetier folder, then closed the folder, went back into slicer, made a new profile and it seemed to help.
As far as for the threaded rod, it does appear to be a bit bent. I wonder if I were to buy a “straight” 3 foot piece of the threaded rod, and cut a piece off of it, if it would be better…
Also before you print, click the slicer tab, and be positive that the box “override slicer settings” is not checked. For some reason it always is checked every time I open a new file.