Because of the reasons stated by Kef, I would advise against using PE5-7 as GPIO. I've been troubleshooting HCS12s for almost 10 years, and one of the most common design errors seem to be either obscure circuits connected to PE7 / XCLKS, or wrong logic level applied to it at startup.
Please note that Freescale have made some wonderfully confusing documentation over the crystal selection, where they state that XCLKS should be high to select a certain oscillator in the oscillator part of the manual, while at another place in the device user guide, they say that PE7 should be low. The secret trick here is to realize that the Freescale manual actually isn't contradicting itself, because XCLKS is referred to as /XCLKS in the real world outside the manual, it is an inverted signal.
Plenty of HCS12 designs have failed because of this - if you pick a Colpitts oscillator but have a Pierce outfitted on the PCB, the CPU will disapprove, but start up in self-clock mode ("limp home"). 5V on PE7 pin at startup = Colpitts, 0V on PE7 pin at startup = Pierce or external oscillator.
