Problem setting home and getting Ender 3 basic geometry dialed in

I have the following hardware configuration:

1. Ender 3 Pro
2. SKR E3 Turbo
3. Ender Extender 400XL
4. BLTouch
5. BTT TFT35 E3 v3.0 (Marlin/LCD and BTT/BLTouch configured)
6. Dual Z steppers (per Teaching Tech, example 3)
7. Dual linear rails on Y-axis (adapters by printermods.com)

I plead guilty to having too many mods on this machine but everything was working until very recently.

After installing the linear rails mod, I discovered that the Y-axis movement was inverted in Marlin. I fixed that but (as of now) I can't get the device to home using sensorless homing (in Marlin mode on the TFT35) using Motion ▶ Auto Home. The gantry moves toward the (now disconnected) X-axis endstop switch (far left) and keeps buzzing until I press reset on TFT35 or cycle the power. The Y-axis seems close to appropriate. Marlin shows sensorless homing enabled/defined for the X and Y axes and the appropriate Diag pins are jumpered for the X and Y TMC2209s.

Additionally, the Z-axis seems to "think" the nozzle should be some 45 mm above the bed. This being so far off, the BLTouch doesn't ever get triggered so as to define a soft endstop.

Specifically, executing a G28 Z results in an X and then Y gantry excursion to the apparent soft endstops, then to apparent X, Y - 0,0, then centering at X, Y - 200,200 (my bed is 400 x 400 mm). The nozzle then raises to an indicated 0 (i.e., 200, 200, 0) which is approximately 40.1 mm above the bed.

At my age, I know I am at wit's end when I voluntarily go out and mow several acres of lawn in the oppressive Georgia August heat.

Sorry for the long, rambling soliloquy. I would greatly appreciate any insight or other assistance anyone might offer.

• What is the actual Z axis movements when a Z home is commanded? As in a rough estimate of distances and directions it moves. Aug 7, 2021 at 23:43
• I submitted a edited of your first paragraph for clarity, feel free to further edit or revert my changes. Aug 8, 2021 at 0:01
• Please see edits added in response to questions by kezat. Aug 8, 2021 at 12:39
• To be clear. Sending a G28 Z command will cause all three axis's to move? Makes me think this is more then just trouble getting the thing to home. If you send G92 X0Y0Z0E0 (to set all axis to zero) then try a independently move each axis such as G1 X100 will the single axis move alone and in the expected direction? For this test to prevent damage manually move the extruder a safe distance from the bed/endstops before attempting. Aug 8, 2021 at 19:08
• Sent M211 to disable soft endstops. Manually moved nozzle to front, left corner and surface of the bed. Sent G92 X0 Y0 Z0 E0 via Octoprint Terminal. Manually (using TFT35 Marlin mode, move axis ) moved the extruder/nozzle to X 200.00, Y 200.00 and Z 200.00. Then sent (individually, from Octoprint Terminal) G1 X100, G1 Y100, and G1 Z100. Results of individual G1 moves were: Aug 8, 2021 at 20:42