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Bed leveling and offset
When I level my printer bed I use a piece of paper, home the Z axis and make the distance between nozzle and bed so that the nozzle just starts to pull the paper.

Now, from what I understand this means a distance of approximately 0.1 mm. However, when I start a print with 0.3 mm layer height, the Z goes to 0.3 mm (as it should, I guess). This however means that the nozzle is now 0.4 mm away from the bed. Thus the filament will not be squished to the plate. This is actually what I see on my current prints. They do adhere to the plate, but they are not squished remotely as much as the ones I did with the stock XYZ FW (and which gave a nicely squished first layer).

Now, I could of course try to push the nozzle even closer to the bed during calibration, but I will never be able to get closer than 0 mm (obviously). Should I instead try to fiddle with Z home offset in the EEPROM setting or am I using the correct calibration method?
I tried many different options. I get the best prints when the extruder is leveled right on ( touching ) the glass. You will know if it is to close as you will hear " clicking " if the plastic can't come out of the extruder.

I added 3mm nuts to the bed adjusters to prevent any movement after I found the perfect height.
I don't adjust the bed level with the printer homed. I do it with the bed at the first print level. For example, if I am printing at .35mm for the first level, I set the bed at .35, heat up the nozzle and bed and then adjust for the paper or in my case, a business card. This is how I do it using repetier. When I was using the XYZ software, I would start the demo and as soon as it started to print the front right priming piece, I would switch off the printer, level with the paper/card at the 3 points and then turn the printer back on and send my actual print.
You shouldn't turn the printer off to do the calibration because the moment you do that both extruder and bed will cool down quite fast and thus the gap between the two will change. You need to do this with stable temperature.

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