It looks to me like you're trying to print the first layer too thin (even for 0.1mm!) - I'd highly recommend setting your first layer to 0.2mm for the moment, get that dialed in, and then attempt 0.1mm (it's quite tricky to get right out of the blue).
When levelling the bed, the feeler gauge is great - but to get the first layer height right, the only way I've succeeded is to then print a skirt / single wall on the bed, peel it off, and measure with calipers - adjusting the z-stop to bring the whole (level) bed up and down until it's right. And for adhesion, I often aim for my first layer to be a bit under theoretical height too (e.g. 0.20-0.22mm for 0.25mm first layer).
Note that Z=0 is theoretically nozzle-touching-bed (zero gap), the printer will move to Z=first_layer_height to print the first layer...
So you've done the 100mm extruder calibration? I'd follow this up next with:
* Measure actual filament diameter, enter this into slic3r filament settings
* Print a single-wall calibration cube, and use the slic3r extrusion multiplier (filament settings again) to achieve the correct wall thickness (as IronMan described).
Then you can proceed to ensuring that first layer is correct! 
SD3. Mk2b + glass, heated enclosure, GT2 belts, direct drive y shaft, linear bearings, bowden-feed E3D v5 w/ 0.9° stepper
Smoothieboard via Octoprint on RPi