Makerbot Replicator 2 Alignment Problems

If your Makerbot misaligns from one layer to the next, chances are you have a bad cable on either your X stepper motor or your X endstop sensor.  The cables are a little time consuming to replace because each cable attaches to X, Y, and Z motors or end stops, and feeds to the motherboard under the machine.  I replaced it with cables from Robotshop that have a connector to a small jumper cable on the X motor and X end stop.

Replicator 2/2X Cable Assembly E - XYZ Motor (Rev2)

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Replicator 2/2X Cable Assembly D - XYZ Endstop (Rev2)

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You also need the jumpers that make the last part of the connection - this is the part that fails due to the repetitive strain on the cable.  You need to buy at least one of each, but better to buy several so you can replace it quickly next time it happens.

Replicator 2/2X Jumper Cable - X Motor

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Replicator 2/2X Jumper Cable - X Endstop

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If you experience intermittent X axis motion, or grinding when the system does "Home Axes", this will solve your problem.