Help with circle/XY calibration

Yes I did (shortly after my original post) and while it helped substantially there are still slight flat spots at the same locations.  But I can now get the nickle to fit.

I still can't get the nickel to fit, but at least its really close to square. I'll try another slicing program too

What is your extruder steps per mm set to?

I had to bring mine down to 95 to get the nickle to fit. I read somewhere that normally it is around 110...not sure if this has to do with my E3D hotend or if I did something wrong, but I do get 38.10 outer diameter and the nickle fits.

I will have to download Kisslicer and try it, Skeinforge seems overly complicated (but maybe I will try it since it is included with Repetier Host).  My E steps are at 108.7 which was obtained from the extruder calibration from Ians blog (the straw method) and my extrusion multiplier is .81 which is needed to get accurate wall thicknesses.  I due have to reduce the flow rate to get the nickle to fit but that does result in improper infills.

The slight flat spots aren't that big of an issue for what I am doing right now.  My biggest problem is random and unexpected over-extrusions.  Every once in awhile it seems more plastic is extruded than should be which results in blobs along the exterior and/or bumps on the surface which causes the nozzle to catch and shake the build platform which increases the problem to the point where the build eventually gets knocked loose from the platform.  Could this be caused by variations in filament diameter?  Right now I am using Octave red which does seem to have significant variations in diameter (as much as .5 mm or more).

I am still tweaking the settings and it seems that each filament I use requires different settings.

I enabled that for a print that had many small parts that the extruder kept knocking over and it worked wonderfully.  But I read somewhere that it is hard on your Z axis motor.  I guess that it can't be that hard though as the X and Y axis are constantly moving and they are fine.

How much lift do you put on Z?  When I did it I put 1mm.

But that isn't my problem though.  I think that the problem is the Z axis doesn't do the proper steps on layer change.  I had the Well Nut Z wobble fix on it and think it might be causing it to jam.  I have taken it off and will test without it.  If that doesn't do the trick I might try upping the Z axis current to give the motor a bit more push.

What do you guys think?