Help with Gantry Rebuild and diagnostic of layer alignment issue

I have been having an issue with layer misalignment when printing. What is interesting is it seems to be tied to the z-seam setting in cura. When I print a 25mm calibration cube with the setting set to "random", every few layers I will have a layer that extends out about .5mm to 1mm on two sides of the cube. It is always the same two sides that this occurs on. When I change the setting to "shortest" with "hide or expose seam" the problem disappears and the cube prints perfectly. This problem is not material-specific (that is, this occurs with every material I try with".

I recently undertook a gantry rebuild and am wondering if it may be tied to that. When sliding the extruder along the axes I feel like I am getting more resistance than I should. One potential issue is that I failed to make a note of the specific orientation of all the pulley bores and the different-sized black spacers that go between them and the gantry before disassembling. I tried to figure it out the best I could and they are currently oriented in such a way that each belt is about 22mm from the wall. I have tried to look at pictures and videos from different threads but has been a difficult task getting the whole picture. If someone is able to take a picture of each corner of the gantry I could try reassembling it the way it comes stock from the factory. The other potential issue I can think of is that the rods may be bent, I didn't replace those when doing the rebuild.

Or if anyone has an idea of what else may be causing this problem I am obviously open to that as well. Any help would be much appreciated. I will try and upload a picture within the next 24 hours.

 

This problem is often tied to over extrusion on my machines. Depending on the filament I have gone down to 84% extrusion on the outer layer and 86% on the inner layers. It makes no sense to me but it often solves the problem and gives me a much finer finish.

I posted the STL's for all of the spacers in the gantry with each spacer having it's position embossed.
http://community.robo3d.com/index.php?threads/carriage-spacers-for-the-r2.23806/
This makes re-assembly easier and everything lines up.

 

I was tuning up one of my production parts with a new filament and had the same problem. Knowing that my R2 printed fine with a different filament I began exploring what settings caused this. There are three settings that have and effect and in the order of effect: Flow Rate, Temperature, Speed. The lower the flow rate the finer the finish and less the effect. On some products that do not require great mechanical strength I have gone as low as 70%. As the temperature goes up the effect is less. A 5C increase can be the repeatable difference. I have gone down to as slow as 20 mm/sec to get rid of the effect.