Z artifact diagnosis help

[jrlowe]

My 3d printer is a prusa i3x which I have had for a little over a year. Over the course of that time, I have made many upgrades, improving the print quality. The last thing I can not work out, which has stumped me for months now is z artifacts, which I have dug online for hours but all the answers are things I have tried. Here are upgrades I have made:
-got rid of low quality threaded rods and go 8M 2mm pitch ACME Leadscrews which run very smooth and straight
-brass antibacklash nuts for the rods
-aluminum flexible coupling
-decoupled the x carraige from the z axis (custom made decoupler) (This was designed to prove that the problem was not z wobble, for, the print quality it the same)
-Constrained the top of the leadscrews with 608 bearings (with and without yields the same problem)
-reprinted elliptical (bad) extruder gear which came with the kit
-calibrated extruder (calibrated very accurately)
-Tried with cooling fan on/off, heated bed on/off
-printing the same object normal speed, and very slowly (- 10 mm/s) and the quality was the same (which I believe rules out vibrations and backlash)

As you can see below, I vertically lit a Z resonance test print, revealing ugly misaligned layers.
In this print I:
-printed very slowly
-heated bed off (to prevent expansion & contraction of glass)
-Makerbot PLA @205 degrees
-.25 mm layers (rounded based on reprap calculator)
-Made 2 towers at different speeds, (normal and very slow (this one) and they turned out the same)
-had cooling fan on

Z wobble would indicate that the big bands are evenly spaced, matching the thread pitch, but I did not notice any repeated banding, or anything matching my leadscrews.

One possible culprit could be my hobbed bolt as seen here:

which is slightly not concentric, but there I don't believe such artifacts could be caused by this.

Printing at lower layer heights like .1 make the bulges smaller and less noticeable, but they are still there.

To rule out more possibilities, I calibrated my z axis steps based on my leadscrew, stepper drivers and motors, which is not rounded at all. I also used a calculator on reprap to find the optimal layer height for my z axis setup that will result in no rounding errors over time, which I used in the print.

If anybody knows what is going on here that would awesome! I've been pulling my hair out trying to get this thing figured out.