The SKR v1.4 has the uart mode connected via the second row left set of pins where as the SKR v1.3 has the UART on the outside of the stepper driver sockets. All of this seems to be working fine. I can read, change values to it all. My TMC2208 doesn't have additional pins, like the TMC2209 have. And I have tried replacing the TMC2208 with a TMC2209, And bend out the diag pins, as you suggest.
The issue I am having is that, my probe works fine, just up to the point where the board receives G29, then somehow the pin connected to the probe (no matter which) goes low, and in triggered state, even though the probe isn't lighting, and no metal is near it.
Might try to start over with a fresh marlin, perhaps the bugfix version.