I'm glad to hear that you will be iterating over your product. I suppose I underestimate the inefficiencies around using LinkShare.
But I hope you'll be able to use my comments as a way to improve at least your messaging. At it is now, it's really as if bit.ly were adding their Amazon code every time they were shortening an Amazon link. To some people, that would make them a great business. To me, it's just shady.
This may just be a case of wording, we started as a bit.ly for iPhone apps, and moved into the services for iPhone developers. If bit.ly would offer a premium service where you use a subset of their URLs (say, bit.ly/app_XXX) and they put in affiliate codes so that they can track your sales data and give it back to you, people's reaction would be 'sweet, more features from bit.ly'.
If you really want to do the hard work of getting all the analytics we provide setup your self here is a blog post for you...
http://shanecrawford.org/2009/119/tracking-appstore-conversi...
We have a dedicated group that is going to be adding a bunch more cool features to the appsto.re service. Give us a shot we are here to make the service a valuable tool.