Cookies aren't plugins; they're browser-specific and you'll need to re-login to the sites you have cookies set at so that the cookies can be re-set.
As far as Flash, I think that should all be set up. It is on my Linux install and I'm pretty sure it is at home as well (I use a Linux workstation at work for a lot of stuff, but Windows at home 'cause I only like Linux if I'm getting paid for it). If it's not, you'll need to download the plugin from
http://www.macromedia.com/go/gnavtray_dl_flashpl
Installation is pretty easy, and it's only a few hundred K, or a fraction of an MP3. So don't worry about it.