Hi Rickl,
Debugging your Stop mode code can be tricky, as you have found out because the BDM is not too useful. An ammeter connected to VDD is often the best way to work with Stop modes. You basically figure out the expected current draw (Idd) for your setup, write & run your code, and measure Idd to make sure they match up. I suggest starting off with static tests that initialize the MCU and just put it directly into the desired Stop mode. Make sure you disconnect the BDM when you are taking current measurements. I haven't worked with the Spyder08, so this may not be easy. Maybe bend the VDD pin up on the MCU to make the ammeter connection, if possible.
I haven't tried going into Stop mode from an ISR, but it sounds like it should be possible. I have seen that you usually do some work then hit the Stop instruction. You then wait for an event to wake you up from Stop mode, and do some more work. An ISR is sometimes used to wake you up from certain Stop modes on a periodic basis.
Getting into the Stop mode is the first problem you face, then getting out of Stop mode is the next step. The 9S08QG Data Sheet is the best source of information for you with respect to understanding Stop modes. I suggest you spend some time looking through the information in the Data Sheet, because it will actually save you some time when working with the Stop modes.
Lastly watch out for the write once bits in the system configuration registers. This can be tricky, as you really end up with a write once byte. If you post the appropriate sections of your code, I can look for the typical problems. Start off with simple tests that use an blinking LED or GPIO when working with Stop modes.
Thanks,
Rick