It sounds like a startup program is causing these slowdowns; do you have other accounts on this computer?
If you do, try logging on to those accounts and do they slow down.
If you don't have another account, go to System Preferences -> Accounts and create a new account; then log out and log in with that newly created account. Again see if it's an instant start up or does it take 5 minutes.
If the problem goes away, you know it's regarding you account; now you can go back and delete the new account you created. Now when did you start having this slowdown and do you remember when it happened after install what?
If it doesn't go away; well it would appear something is wrong with your whole computer; two solutions to see if it's hardware related. If you have an external HDD, you can create a small partition on that and install OS X on it; if it's slow and weird, you know you've got a hardware issue and it's time to take it to Apple. If you don't have an external HDD, you will need to back up your files and do an Erase and Install, but I'd hold off on that and contact Apple first.