I have a FT 5-1 upgraded to a -2 running Marlin bugfix 2.0 and a SKR V1.4 turbo with BTT-TFT35-V3.0 with steppers 2208 in standalone mode
Y-steppers are separated, one on Y and one on E1.
All steppers in 1/16 MS, 4 jumpers installed on the right as shown here

End-stops are standard that came with the unit, here is what I done so far,
Did compare the 2 .h files that were in post
http://folgerforum.com/t/skr-v1-3-controller-tmc-2208-marlin-2-0-works/2495/11 and 14
Also the official ft 5 version .h
define X_HOME_DIR 1 gave me error in sanitycheck
error "Enable USE_XMAX_PLUG when homing X to MAX."
With the touchscreen I can move all 3 axis as indicated on the screen right arrow x moves right and so on.
But homing the X goes the wrong way and slams away from the endstop.
When activating the limit manually the driver stops, led on, this goes for X Y and Z.
I reversed the rotation of the X in the firmware and did a test, homing works now,(moves to the right) but on the touch screen I have to use the left arrow to move to the right manually.
Thinking now that I might have to find a solution in the operation of the touchscreen.
This is why
// This option reverses the encoder direction for navigating LCD menus.
// If CLOCKWISE normally moves DOWN this makes it go UP.
// If CLOCKWISE normally moves UP this makes it go DOWN.
found this under LCD and SD support.
Z-Axis,
When checking marlin there is a link to https://blog.prusaprinters.org/calculator_3416/
Here they are trying to talk you out of using micro steps:
"Optimal layer height for your Z axis
Helps you to select layer height in a way, that Z axis moves only by full step increments. Z axis isn't usually enabled during inactivity. If the axis is disabled during micro-step, axis jumps to the closest full step and intorduce error. This effect is occuring to some extent even while leaving the Z axis motors enabled. This is most usefull to machines with imperial leadscrews but also for unusual layer heights with metric leadscrews."