Hi Peter,
Let me answer your latest questions. And don't worry, everyone started as a sometime newbie for something.
1/ MMA9559LSWRM describes the overall framework of the proprietary Firmware provided with the device. So it does not explicitly details how the cube demo operates. As Anthony already mentioned: "modify the section between line n°126 and the end of the kube.c file" to customize the LED colors.
2/ USB Multilink Universal from PEmicro is a reliable and proven BDM interface for ColdfireV1 MCU such as MMA9559L. I'm not aware of simpler/cheaper alternatives officially supported.
3/ download below reference (if you have a Windows machine)
Special Edition: CodeWarrior for Microcontrollers (Eclipse, Windows hosted) - Code Size Restriction: RS08/HCS08 - 32KB, ColdFire V1 - 64KB, ColdFire V2-V4/Kinetis - 128K, MPC56xx – 512K
Regards, Jacques.