I think SolidoodleSupport identified the issue, at least in part. I checked the extruder multiplier and it was set to .78. I changed this to 1 and printed a single wall print and it came out great. I went back to the nickle calibration print and it no longer fits. My result was ~20.46 ID where I should have 21.21. OD is still about right(~38.15). I came back down to .90 multiplier and didn't have much luck..fix one thing break another. Is there another setting I can change that would correct the ID while leaving single walled prints accurate?
I switched back to Octave black for a couple test prints to see if it was a factor. Once I realized the extrusion multiplier was in fact the issue i switched back to Octave red. First image below is .78, then 1, then 90.

Current Settings in Repetier & Slic3r
Steps per mm: X:87.18 Y:87.13 Z:2268.00 E:97.44
Filament: Diameter 1.69 Extrusion multiplier: .9
Nozzle Diameter: .4
Hotend: E3D with .4mm nozzle
edit: What appears to be holes in the second image (1 multiplier) is just the bottom of the opposite wall.
E3D-v4 Hotend, MK5 carriage with round plastic wire conduit , 3/16" tempered glass, Well nut, SureStepr SD8825 1/32 Extruder Driver, PowerEdge 2650 500W PS, QU-BD heated bed, circuit board fan, hinged plexiglass enclosure with plastic tray top. Other than that mostly stock SD3