I had to do some similar troubleshooting on my FT-5 R1. Based on that experience, here is what I would suggest:
If you can't get ANY motors to move, I would first do some disassembly, so that you can really test the basics in isolation without other things getting in the way.
* Remove the belt(s) from the Z-axis stepper motor(s). If you have multiple motors, unplug one of their electrical connections as well. This lets you test for bare minimum "Z-axis stepper control" even if you have the two motors wired backwards, mechanical binding in the bed platform, bearings, or belts, stepper driver voltages way out of whack, etc.
* Remove the belts from the Y-axis stepper motors, and remove one of the two electrical connections, for the same reasons. (As long as the carriage moves smoothly in the X axis, you should be OK to leave that one connected.)
* Don't worry about the extruder stepper until after you have resolved all of the thermal/heating issues. Marlin has a safeguard that prevents "cold extrusion"... ie: it won't try to force filament through a hotend that is under a specified temperature, as it wouldn't be able to extrude and would just grind the filament, skip steps, or break things. So save testing the extruder until after you have the heating working. (This one caught me off-guard as well when I was testing my FT-5.)
* It would be best to test the extruder without filament loaded when you get to that point. That way, you can advance and reverse that stepper as much as you need to, without worrying about jamming the extruder from an over-retraction, cooking filament in the hotend if it sits too long without extruding, etc.
* Verify that the three endstop switches are connected and correctly wired. They each have a red LED which lights up when the switch is triggered, so with the printer powered on, this is easy to test by hand-pressing each switch and checking for the light.
Beyond that, here's a few additional suggestions:
* For your initial testing, unplug your USB cable and do everything from the printer's LCD. Trying to use the computer only complicates things - It's just a whole range of software and connection issues that you can immediately rule out if you work directly from the printer, and the Marlin menus provide everything you need to fully test out the printer mechanics and electrical systems.
* Related to that, forget about 3D models, slicers, and all of that for a while. None of it is needed for the basic printer setup - even a fair chunk of the calibration can be done without ever needing to initiate an actual print.
* Note that the Marlin firmware disallows certain movements until the printer has been homed. For example, if I manually push my print carriage to the center of the build plate and then power on the printer, Marlin establishes the current point as "zero" for the X/Y axis and will not let me command the steppers to any "negative" value. So if your carriage hasn't yet been homed, it could be that you have attempted to "test" the steppers by commanding a certain direction, and get no response simply because of the expected firmware behavior. (Marlin will allow for moving each axis both directions before homing- it just has to move a certain amount in a positive value first, and won't ever be able to move the return direction any amount past its zero-value power-up point.)
* Likewise, AFTER an axis has been homed, the firmware won't move that axis beyond the endstop. So again, a new zero point has been set, and your manual controls will only be able to move the axis one direction from home. They can return of course, but trying to move negative values from home will have no effect.
* Don't forget to calibrate the stepper driver voltages (which in turn control the stepper currents). Them being too far out of range could cause the motors to not respond as expected.
* Once you have at least one axis responding, if others are still causing problems, you now have what you need to start isolating the cause, by swapping the plugs between each axis on the controller. For example, if the X axis works but the Y axis doesn't, you can swap the plugs on the controller between them. If the Y axis then works (when commanding an X change), but the X axis does not (when commanding a Y change), then you likely have a board or stepper driver problem. But if the X-axis continues to work and the Y-axis continues to not work, then you can be reasonably sure that it is a wiring or motor fault. DO NOT TEST THIS WAY UNLESS YOU HAVE DISCONNECTED THE BELTS.
You never mentioned it in your post... Does Marlin boot correctly on your board? You said it uploaded OK, but the rest of your diagnostic notes were from the perspective of the PC software, and connectivity issues or software bugs could certainly cause that data to be incorrect or misleading.
Arduino version 1.6.12 should be fine. It's the version I use, and I've been successful with dozens of modifications and uploads of the original Marlin 1.1.2/1.1.3 firmware as well as the newest 1.1.8.
Hope that helps - good luck!