Hello, I was wondering what the steps would be once you discover a botnet.  In the USA is there an agency to report it to that would actually make an effort to investigate and pursue to botmaster or is it more of the kind of thing that gets reported, entered into statistics and forgotten about?

http://www.shadowserver.org This organization is a good place to start.  It is run by volunteer Info Sec specialists.  They track and analyze bot nets.  They also coordinate with the proper agencies, US and International, to get the bot nets shutdown when they have gathered enough information.

Might be worth passing the info to the SANs Internet Storm Centre. If they aren't able to look direct they should be able to put you in contact with the right people.