I have purchased a Replicator 2 with Mightyboard revH. There were connection problems, Y axis pulley missing and a bad LCD module. I got ReplicatorG 40 and I was able to move the all axis except the X in negative (left).

Swapped cable, BotStep board and stepper. - No luck on any of them

Checked limit home switch and it works correctly - No Luck

Put new firmware 7.6 Sailfish - No luck

Inverted the X axis and it moves left. - not a solution, won’t move right

Checked if the BotStep get Vcc 5V at direction pin. All Good. - No luck

One interesting thing I noticed. When trying to move it to the left it almost appears as if wants to move but something is preventing it (Software). I hear a little clunk every time a I click on minus jog button. This was interesting and I held the limit switch (X) and then it did it both directions. No movement left or right, just a little clunk when hitting jog buttons. This tells me that that the X axis seems to be prevented from moving left (-X) by the micro-controller. A very strange problem. Anybody has any advice I would appreciate it.

Have you tried swapping the x & y axis? This would help to narrow down the cause.