Speed up Linux booting using IDE CF card alongside regular sata hdd.

It sounds very simple to me -

Install the bootloader and an initrd image on the CF card, and the final root system on the HD. That will cut down your boot time, although your normal running time won't be affected.

You will probably have to do this by hand and then write a small script to do it later. Basically, the CF has the bootloader and a small partition to hold the initrd image. Whenever you update components that normally go into initrd (kernel, udev, module init tools, etc) you will need to generate a new initrd, mount the CF, copy the initrd, and if you use lilo you need to update the bootloader. Leave a copy of the initrd on your root system so if anything goes horribly wrong with the CF card you can still use an emergency boot disk to get your system running from HD again.

The Debian initrd is extremely basic - for what you're doing you may even consider creating your own initrd with extra scripts etc. This is actually fairly trivial to do because you can simply alter some configuration files to make the initrd creation scripts add all the extra bits you want.