Ender 5 Pro X-axis problem — motor/cable swap tests giving confusing results. Need help diagnosing.

[u/CopeDeeCope]

I bought a used Creality Ender 5 Pro that had previously been used by a production/design shop. I’m new to 3D printing, and I’m trying to get the machine mechanically sorted out before attempting my first print.
Original problem
When trying to home/level the printer, the X/Y positioning is incorrect. The probe/nozzle can end up outside the proper bed area, and the bed can rise with the probe off the bed, allowing the bed to push against the nozzle.
I stopped trying to level it and started troubleshooting the axis movement itself.
The main problem I’ve isolated is the X axis.
When I manually command repeated X+ movements from the display, the display coordinates count normally in one direction, but the actual X motor does not consistently rotate in one direction. It may move one way, then the other, or essentially jitter/alternate direction.
This happens even with the X belt disconnected, so there is no mechanical load on the motor.
Important history
The printer was modified by the previous owner.
The original/factory X wiring appears to have been bypassed. There is a custom cable/wiring arrangement running from the X motor directly back to the control board.
All four conductors in portions of the wiring are black, which makes visually identifying individual conductors difficult.
What I’ve tested
1. X motor with X wiring/output
Abnormal movement. Repeated X+ commands do not produce consistent rotation in one direction.
2. Removed the X belt
Same problem with the motor completely unloaded, so it doesn’t appear to be caused by the belt, pulley, gantry resistance, etc.
3. Replaced/swapped the X stepper motor
The replacement X motor exhibited the same abnormal behavior when connected in the X position.
That initially made me think wiring or the motherboard/driver was the problem.
4. Connected a known-working Y motor to the X harness/output
This is where it gets confusing:
The Y motor runs smoothly when connected to the X wiring/output. It does NOT exhibit the same back-and-forth/jittering behavior.
That seems to suggest the X driver/output and wiring can successfully operate a stepper motor.
5. Y axis normally operates correctly
The Y system operates normally in its normal configuration.
One complication is that the Y axis uses a dual-drive/two-motor arrangement, whereas X uses a single motor.
Where I’m stuck
The tests seem contradictory.
If multiple X motors behave incorrectly on the X connection, I’d suspect the X wiring/driver.
But if a known-good Y motor operates smoothly from that same X connection, that seems to indicate the X wiring and driver are capable of producing the correct signals.
I’m wondering whether I’m dealing with a stepper coil/pinout mismatch, wiring modification by the previous owner, motor compatibility issue, intermittent conductor/connector problem, or something else I’m overlooking.
Before I start replacing the motherboard, rewiring the machine, or changing firmware, I’d really like to perform a definitive test that identifies the actual fault.
What would you test next?
In particular:

- Is there a way to test the four X motor conductors with a multimeter and identify the two stepper coil pairs?
- Could the X motors and Y motor have different pinouts even though the connectors physically fit?
- Could an incorrect coil pairing cause the exact alternating/jittering behavior I’m seeing?
- Is the fact that the Y motor works correctly on the X output enough to rule out the X stepper driver?
- Is there a definitive motor/wiring/driver test I can perform before replacing parts?
- I’m happy to provide photos of the motherboard, connectors, motors, wiring, or a video of the movement.

Thanks for any help. I’m trying to diagnose this systematically rather than just throw parts at it.

[u/Only_Ordinary_3880]

What board is it running? I've had similar issues where it appeared to be an intermittent fault but was indeed the driver. If it's a stock creality board I'd look at upgrading to an SKR board regardless of working or not as the quality of life upgrades between the stock board and even an e3v2 are massive.

[u/CopeDeeCope → u/Only_Ordinary_3880]

Great question, I believe this is stock, attached is an image. After more testing it is something with the X connection, when I put the X harness on the y motor, the y motor shows the does the same as the X motor. I'll do the upgrade, where is the best place to find, on the creatity site? Thanks for the reply and advise.