I don't think it's the first layer height, here's the back side of the first layer, looks like plenty of squish:

And then the second layer:

Kinda looks like the perimeter is OK and the infill is way too low?
I have the E3DV6 hot-end with an 0.40 nozzle, and am printing at 240C as per E3D recommendations, bed at 100C
My settings are (defaults where not specified):
Slic3r 1.2.6
Layer height: 0.1976
First Layer Height: 100% <---- Default 0.35
perimeters: 3
Horizontal Shells: 4 Top, 4 Bottom <--- Default 3
Extra Perimeters if needed: Disabled <--- default enabled
Seam Position: Aligned
Infill: 100%, both patterns Rectilinear
Skirt: 1 @ 3mm, height 1, minimum 10mm of filament
Brim: No
Support: No
Speed: untouched Solidoodle defaults (not Slic3r defaults)
Advanced:
Defaults:
First Layer 200%, all others 0 for defaults. Same thing happens when everything set to 0.48
Threads 9 (8 core CPU)
Filament Settings:
I'm using Monoprice Orange, if that matters
Diameter 1.70
Extrusion Multiplier: 0.923 (Note that this gives 0.48
Printer Settings:
Nozzle Diameter: 0.4 mm
Printer:
Steps per unit:
M92 X88.00 Y88.00 Z2268.00 E97.00 <---- Originally E138, way overextruding
Clearly I screwed something up when I rebuilt the printer and changed the stock SD head for the E3DV6, but exactly what is wrong?
Thanks All!