this post was submitted on 19 Aug 2023
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If i understand correctly, your nozzle is too high still even with your Z at its lowest value? You should be able to follow these steps to adjust it lower (under "I've added a BLTouch, how do I set my Z-Offset"): https://marlin.crc.id.au/forum/t/ender-3-v2-frequently-asked-questions/17#heading--zoffset
I still use Z clickers instead of CR Touch. My lowest low with the clicker/lever makes the Nozzle stop below my bed. I could remove the glas bed to shrink my bed and maybe put a metal sheet on it or purchase a thin plate, but with the glas bed, the lowest Low I can get with all the 4 corners is not low enough for the nozzle to not touch the bed.
The steps are the same regardless of what you're using for a Z sensor. The only issue I see is if your limit sensor physically won't allow the gantry to move lower due to its mounting position otherwise it's a 'soft limit' set exclusively in the firmware (which the above steps allow you to reconfigure).