The I-Opener only supports 2 IDE devices at a time. The built in "disk" that holds the QNX OS that the I-opener ships with is on one of them , so if you plan running 2 drives as you described you'll have to install an OS on the hard-drive and boot from it.
I've not messed with QNX too much, but I doubt you'd find DVD ripping software for it.
Modwise, to start with you're best going to badflash.com and ordering the relevant IDE cable and BIOS from him, the basic mods to get the machine going aren't too bad, it's all screwdriver work
Before getting to involved in this, bear in mind that the I-Opener isn't exactly the fastest machine around, I wouldn't like to guess at how long it'll take to rip a DVD, and you can forget playing one back on it, the screen sucks.