Thanks a lot for answering my question. For the moment I plan to use the iPod only with this amp, and because I plan to put the caps outside (most probably directly on the cable) I can play around with caps (rating and types). And as a bonus the caps are almost half the price :)
Because it will not be a mobile solution I'm thinking that most probably I will route the signal thru the headphone jack. The iPod usually stands in the dock and I have opened yesterday night the dock hoping that the line out jack comes directly from the bottom iPod pins, but unfortunatelly it seems that first goes thru a integrate ... I will try pull the pcb out in order to inspect it visually and/or measure the path woth an ampermeter.
That's a good idea to have the caps so you can change them, experiment, etc. It also is worth mentioning that if you only need 1uf caps, stick with it. The is a disadvantage to using more cap than you need... (4.7 for example) - there is more material in the signal path. Less material, the more pure the signal. At least that's the way I understand it. The whole point of this mod is to get the pure signal from the DAC, so the less capacitance in the way, the better.
It would be an interesting experiment to have two identical setups where one was a 100k amp and 1uf caps, and a 10k amp with 8uf caps. Then see which had a better sound. My guess would be the 100k amp and minimal capacitance in the path. However, this experiment would never work because the character of the different amps would screw the whole comparison up!