I suggest you use MC56F84xxx or MC56F83xxx for example MC56F84789, which has 2 eFlexPWM modules, 2 quadTimer modules.
The tools for DSC is CodeWarrior for mcu ver11.x, this is the link:
The debug device is USBTAP, this is the link:
You can order the EVM board for MC56F84xxx, the link is:
The power stage board is:
For the encoder, pls refer to an4813.pdf:
The KV family is an option, the FTM modules can generate PWM signal and function as decoder for example KV11, KV31.