First off, I want to say that software is awesome, thank you very much. Now this is just an idea, you could call this a helpful suggestion. The iphone has really clean audio connections from what I have experienced, but apple has a cable which may work better than using the headphone jack. Now maybe this won't work, and I don't know if you really want to do it, but there is a 30 pin connector that you can plug into the iphone. The one I had was made to cover every input channel to the DVD player HD, and then connect the 30-pin to the iphone.
http://store.apple.com/us/product/MB129LL/A?fnode=home/shop_ipod/ipod_accessories/cables_docks&mco=NTQ4OTg That cable is a composite standard A/V cable, that probably could work for what you are wanting to do for input. That could also have the cable from the from the computer for a power source/possible input, into the 30-pin connection line pre-composite hook in.
http://store.apple.com/us/product/MB128LL/A?fnode=home/shop_ipod/ipod_accessories/cables_docks&mco=MTM1MTc Now that is the one I have, now maybe you could find something to do with the extra (Pb, and Pr), possibly, I am not sure, I should read up on it, but, maybe that Pb and Pr line could hook into the iphone with the composite sources. Then this could have 2 devices going in at once. I really don't think that is necessary, but hey it is a idea. Maybe that would be useful for a multi channel surround sound setup. I was thinking that the 30-pin connection would provide clean audio to the iphone, vs's a headphone jack. I know I would love the idea of having the option to save a print out/screenshot while measuring an audio level. If you are already at a computer you could just hook it up through another interface though.... All of this maybe unnecessary because you had said you don't know how to hook up through the doc connector, I am not sure if that is a software compatibility issue or if you just did not know how that there was 30-pin A/V cable for the iphone.
Once again, thank you very much for the software, it is a gift to us OCD techie aficionados.
Oh one more thing, I am going to test the 30-pin connector anyways, if it works I will let you know. I bet you were testing it previous to putting it on the market, I will give it a shot though.