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Marlin: Rough Steppers & Failed AutoHome

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Good Evening
This is similar to a number of threads, but different enough to need a new one. I'm experiencing rough stepper motion when using the "MoveAxis" feature, and while the motion is smooth in the "AutoHome" feature, the bed goes to the extreme Y and just continually grinds.
-3D Printer Details:
-- Parts from a Migbot Kit, a Prusa Mendel frame, and a new MKS Base 1.4 Circuit Card. Part of the reason for the mix of parts is that Migbots don't come with all of the parts...as is covered frequently in other posts here.
-- Used 4 end stops (Left & Right X, and Front and Back Y)
-- New Marlin-mks2004 build firmware
-- Capacitance z-axis auto-level sensor (not yet tested)
-Relevant Build Steps
-- Assembled the Migbot Kit onto a Mendel frame, modified the Mendel frame to accommodate the longer Y-axis length for the Migbot.
-- No clear instructions on where to put the end stops, so I figured these out on my own and extensively tested them (see below)
-- The original MKS Base 1.2 with Migbot software pre-installed would continually press down on the heated plate when auto-leveling, so I purchased a new MKS Base 1.4 and tried a new build of Marlin-mks2004
-- Marlin-mks2004 does not compile properly on Arduino 1.6.11, but a quick fix allowed it to compile fine (changing all instances of "fpos_t" to "fpost")
-Relevant Test Steps
-- Checked the motion by using "MoveAxis"--motion is rough, but the movement is the distance noted on the LCD
-- Checked the end-stops by pressing them while turning the dial for "MoveAxis"--for each direction of movement, pressing and holding the end-stop at the extreme end of that axis causes the movement to stop
-- Checked the end-stops for contact when the relevant X/Y axis reaches its extreme (visually, mechanically, and with a multi-meter)
-Problems:
-- The "MoveAxis" is rough, but it could just be over-sensitive to the turning of the knob
-- The X-axis moves as expected (full left then stops) during "AutoHome," but the Y-axis moves full aft then just keeps grinding...until I turn off the power to the system
-Solutions Tried:
-- I've scoured the code but can't find a simple place to instruct "AutoHome" to seek input from the endstop
Any help would be appreciated.

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