From the manual it does not seem to be possible to set or clear the inputs of the State Configurable Timer using a register. It can only be done using physical pins it appears. I think it would be highly benificial to set the inputs in the application code by setting a register for example. The manual says that the SCT INPUT register in read-only (p838, table 665). Is there another way to set the inputs?
I tried using the SPGIO3 and SGPIO12 inputs, routing them using the GIMA to the SCT. While this works, it is still limited to 2 inputs. Another side note with this is that SGPIO3 seems bo be high on reset, which I find strange.
Bottom line: who knows a way to set the SCT inputs in code?