Well, I did "Calibrate" the Z-axis in Marlin firmware and it seemed to move pretty accurately. Such that a 10mm movement signal would cause it to move 10.08mm. I have repurposed Repicator2x, basically my Repicator 2x destroyed it self so I rewired it using an Azteeg board. I had to replace a bunch of 24v stuff for 12v but otherwise it's still got all the same motion control items in it. IE Steppers, drive mechanisms and such.
On another note, a I have printed a few tall objects such, really small things. Such as a 5mm cylinder that is 2 inches tall.
And the Cura test robot print.
So i'm pretty sure z-axis is working at least with enough accuracy that it can print things as tall as 2 inches.
I printed a test print that had multiple geometric shapes and was about 1/2 inch deep. It finished printing but had serious layering issues and most of the shapes looked like they were drawn by a 3 year old.
I have printed the same part in the picture about 10 times with various software including Slicer, using prontface, as well as Cura and both of the had the same results. So i'm sure it's more likely my hardware but the only thing I can think of that would cause a "delayed" error that was not related to the axis is heat. I am not 100% sure the extruder temps are correct because I dont have a great way to mount my thermsistor so it's essentially stuck in a whole in the extruder block. but it has not been sealed in any way.
But just the same, thanks for your suggestion.
https://drive.google.com/file/d/0B0omauD4yWkMcDVnSDliMGVlVlh2RU1MeU14SHptUG1HTnAw/view?usp=sharing
Here is an example of some successes.
Both of them were printed as they stand.