First an admission. I've never use that chip or any MCF51 variant. I've only every used power hungry Coldfire chips running at the full clock rate with lots of external memory and over 100kW of internal combustion power available. I've never used Code Warrior or Processor Expert, so there's no use asking me about anything specific to those, because there's no way I can answer.
But I understand electronics, processors and "know where the electrons go". I've also managed to get an 8-bit ST chip running with a 4MHz crystal down to 250uW, and the experience of that has taught me well.
Assuming nobody else with the proper direct experience of getting these chips down to microwatt levels chimes in, I'll try to help.
> What can I do to have this consumption?
You have to work out from your design and data sheets and by actual detailed measurement where the current is going. There's no quick and easy path. This is real Engineering.
You could also start off with a documented reference design from the manufacturer that already achieves the power consumption you want. That should be the first stage in selecting a CPU if you want it to be easy.
Are you measuring 1mA as the current consumption of your entire board, or do you have current shunts in the supply to the CPU, and are measuring 1mA there?
You have to provide far better details of what you're measuring and how you're measuring it. Providing code doesn't help at all. Providing the register contents of the power control registers would be a good start to prove you're doing the right things. Prove you're following "Table 6-1. CPU / Power Mode Selections".
If the 1mA is the whole board, then your voltage regulator could be drawing that much. If you have a zener across the power supply, then those things leak milliamps, even at half their rated voltages. Zeners aren't actually zeners under 14V or so. What other parts do you have on the board and what do they draw? Do you have any LEDs on the board? They can cause a high current draw if you shine light on them. Yes, really.
You can't measure low power if you have a debugger connected. Low power is extremely hard to debug because none of the usual tools that help with debugging will work.
Prove with an oscilloscope that you've succeeded in stopping the clock.
How are you intending to wake from Stop-2? That might require external hardware that probably draws some power. Are you intending to use the IRTC to wake up? The IRTC has to run from Vbat for that.
Tom