Ahh man I went through the same fog but have only the Gecko 320s not the Camtronics package.
The +5 volt comes from the game port or the computer's power supply; use a ½ Amp fuse close to the source; the computer's power supply puts out some serious current, no need to cook anything.
Can't help you about the "higher powered operation"
Yeah, like Darek said just ignore the ‘index' pin on the encoder.
Yes you can just wire the geckos directly to the parallel ports... 1 step and 1 direction each, no breakout board needed.
There is a bit of a show and tell on this on my site...get there by clicking my name above.
Good luck, it will seem easy once it is done....