Go to F_Secure's Flashback Removal Tool web page, download their Flashback trojan detection/removal tool, and follow the instructions you find there.
Also install the latest java update which also tries to remove these trojans.
Java for OS X Lion 2012-003
And only download the adobe flash plugin from the adobe site.
Update:
Just because you cannot download pdf may not be an indication of the trojan. There's been a number of reports about problems like that with pdf's. Look at the More Like This section on the right side of this page.