Probably the simplest thing to save battery with SetCPU is to set up a screen off profile and drop the CPU down to around 300. Any lower and you'll start seeing issues waking up again.
Check the ROM's and Hack's forum, there are several Set CPU threads there as well.
Will SetCPU work with Skyraider 4.0, or would you have to flash a different kernel? I just flashed SR 4.0, but am fairly ignorant when it comes to kernels, radios, and over/under clocking.
It should, but the autodetect feature might not work properly so the suggested frequencies might not match up with the processor. Do not check the "start on boot" box until you're sure that you have a stable profile.