If you are not directly driving headphones with it, but a headphone amp, 0.47uF should be sufficient under most circumstances. Go for 1uF if you don't want to loose the tiniest bit of bass. And I think that they are really needed... if unsure, you could just do a reading with your multimeter. If the dc voltage is over 5mV or so, you probably need output caps.
I haven't heard blackgates myself, but I must say that I'm a bit skeptical about them. Electrolytics in the signal path? I'd rather go for metalized polyester, they also have the advantage of being readily available at most distributors.
Please post pics if you open up your ipod, I'd be very interested to see the innards. I thought about bypassing the DAC too, but I'm a bit afraid of it.