3DPrinting
3DPrinting is a place where makers of all skill levels and walks of life can learn about and discuss 3D printing and development of 3D printed parts and devices.
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The third photo is the bottom, right? It sounds like you've made the correct conclusion, that you need to calibrate the nozzle-bed distance better. Especially the dark filament looks like it was printed while the nozzle was too far from the bed. However I don't know how you adjust this distance on your printer. On a normal printer with a single nozzle and no probe you would do this by levelling the bed at a different height. On a printer with probe you adjust the "probe z offset" setting in firmware. But since you have dual nozzles there's probably some kind of calibration/levelling procedure specific to your printer that you need to follow. The transparent filament looks like it was printed at a better distance.
I would suggest that you try to improve the first layer before tackling the issues higher up.
Yeah I agree, Id say your white filament has good squish and blue one doesnt. I have 0 experience with dual extruder setup tho. If you are printing PLA glass bed is good
And avoid raft whenever possible imo
Id look at mouse ears as a replacement if you need to stop the parts from warping