Also it just occurred to me that you should also check the squareness of your Y axis to the X axis, as if they are not square this can also lead to stalling steppers, and as you said you have been moving the screws by hand then this is a good possibility to check.

An easy way to do this is to very slowly jog your Gantry to its end stops on the X and they should both touch at the same time on either side, if one side has touched and there is a gap on the other side then turn your steppers off and square it up by turning the screw manually, obviously this will only be accurate to a certain degree but worth a check to start.