Hi Katherine,
1. After exit initialization mode by writing INITRQ=0 we should wait for
INITAK = 0: while (CAN0CTL1_INITAK){};
and Synchronized Status flag where SYNCH = 1 when MSCAN is synchronized to the CAN bus.
2. The MSCAN should not be active when initialization mode is entered.
More information can be found in the section "13.4.4.5 MSCAN Initialization Mode" in the RM rev.2.11
Also, I would like to recommend you the AN4975 Using MSCAN on the MagniV Family
http://www.nxp.com/files/microcontrollers/doc/app_note/AN4975.pdf
AN4975SW:
http://www.nxp.com/files/microcontrollers/doc/app_note/AN4975SW.zip
I hope it helps you.
Best Regards,
Diana