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Upgraded Ender 3v2 Issues

I've had an Ender 3 v2 for a few years now and have had mostly no issues. I've upgraded the hot end to a microswiss direct drive and a dual z setup (twin z steppers on a shared cable).

Recently started having issues with the 4.2.2 board and replaced it with a BTT mini SKR 3 v3.

Since I've put the new board in, I am having troubles getting the bed to level and stay level.

The height profile of the bed is now showing a dip in the centre (which was not there before). When I run a print it seems to be overcompensating for the dip. If I level the bed with the corner screws and don't use the bed mesh then it prints fairly good, but after a few prints the bed goes out of level again.

I can't seem to make any adjustments that help the issue. Yesterday tightened up all the screws (silicon spacers instead of springs). Releveled the bed and had a small dip in the middle and an overall height difference of 0.170 across the bed (normal prior to this was 0.310). Sent a print with bed mesh and mostly came out good.

Went to fire up a new print today and the bed height is showing 0.830 overall difference.

I'm not sure if it is a BL touch issue (the BL touch is a v3.1 and is original with a single 5 wire connector plugged into mini SKR) dual z issue (disconnected 1 in an attempt to level and didn't see much difference, the BTT has two connectors for dual z but run off one stepper driver as I understand it, I am using the y cable for only one stepper motor, while the other motor has its own cable).

I use klipper with a RPi zero 2 w.

I just can't seem to figure out that has been causing the issue since the board swap.

Anyone have some ideas as where to point me?

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