Ah. Now the bot is confused about which motor to stop when it sees the endstop switch. You'll want to get back to where the x-motor is connected to the x connector on the motherboard, but to use your current state diagnostically first:

Don't print or home the printer, only jog. But before you do that move the head by pushing it around with your hands to the middle. Then use the jog controls from the LCD menu. X and Y will be switched, but you should be able to see or hear it skip steps in one direction or the other. If it skips steps left and right now, you need a new stepper cable for the y-axis motor.

If it skips still in the forward backward direction, it's not the stepper cable. Perhaps the y-endstop or its cable.