It seems like the linear CCD would need a combination of the FlexPWM and Quad Time and I am not sure that it is possible.
In the following I connect ΦΜ, ICG and SH, to pins 4,5,6, all on FlexPWM2 submodules 0-2, all of that seems straightforward. For the ADC, the CNVST on pin 10 and the SPI...