In a scanning unit such as a facsimile machine, an automatic document feeder transports individual sheets from a stack of documents along a document path over a scanning window to an output tray. Precise co-planar referencing is provided between a pick roller mounted on a frame beneath a document path and a document separator mechanism mounted on an upper guide member which moves between an open position for allowing manual access to the document path to a closed position for scanning document sheets. An integrated sheet metal chassis on the upper guide member provides a direct reference path between a central portion of the chassis which carries the document separator mechanism as well as Z axis and Y-axis (media transport direction) reference datums on both side edges of the channels which are engaged by a rigid vertical reference arm. A latching device is located closely adjacent to the reference datums to securely hold the upper guide member in a predetermined closed position, as well as determine positioning in the X axis. A pair of pivotal arms at the post-scanning end of the chassis allow clearance in the X-axis and Y-axis while providing secondary referencing in the Z-axis.