I admit I haven't read any of the replies, but here is what I did.
In the kernel you need apm as a module (as you don't really need it for more than shutting down). So enable it as a module and just enable start PM at boot up and RTC stores time in GMT. Leave the rest (and especially leave off the "Use real mode APM.....") off.
Now compile as normal and as soon as you're ready to shutdown, do
modprobe apm
and then:
shotdown -h now
You can avoid manual loading of the apm module by inserting the line "modprobe apm" to your shutdown script (rather than your initialisation since you only need it to shutdown), somewhere in your rc0.d folder