My client's site was attacked too and google sounded the alarm, but it was iframe codes injected to redirect visits to some other sites. And it was due to his ftp password was stolen.
I spent hours with the hosting company and google antimalware team on its forum, but we got it solved within hours. (Goolge removed the alarm flag within hours after we fixed the codes.)
1) ask your host company to check the server log. they usually can spot it immediately, if it is a ftp issue, the server log can tell. there will be ftp log in and out, and ftp download and upload, many times records in a minute time period. These kind attacks usually not done manually but by a software.
2) go to google Malware & hacked sites forum
http://www.google.com/support/forum/p/Webmasters/label?lid=2fe2a8ee8e37c08e&hl=en
posted your questions there, you could get answer from support staff very quickly. sometimes, their response is within minutes. (maybe you want keep your site's name of the thread title, google search will find your thread, you don't want your site name show up with the malware, but you need to give the site in the content to ask them check it out for you)
You are not their paid customer, they don't have to help you so you need to ask smart question and respond to their threads with helpful right on spot information, then you would get your answer very quickly from them.
3) change the ftp password, don't save the password in the ftp client, and use secure ftp instead of just ftp.
4) google search the same attack when you have more info from your host or google forum, it could be ftp or it could be security holes in the 3rd party system you installed but ignored to keep them up to date.