Troubleshooting a slow mac is fairly easy, but sometimes tedious.
You will want to and quit all apps.
You might even go to the Users & Groups preference and remove all applications that start when you log in to your Mac.
Turn off WiFi and then shut down the Mac so you can start isolating it. Remove all peripherals except the keyboard, display and power cord. Power on and then log in and let it run for 5 minutes and then take a snapshot of the Activity Monitor. Look and see what CPU usage is and if the background tasks are taking any CPU time.
If so, dig deeper - open terminal and run "sudo sysdiagnose"
If not, go ahead and connect your peripherals one at a time.
Check the CPU/Activity Monitor and watch both the Memory Pressure graph and the CPU. If you want, you can also look at energy, but that's better for half hour snapshots for me.
At this point, you should know the OS is fine and all of your peripherals and hard drives are not causing the slowness.
Now go ahead and start the apps you choose to run when it's slow. Again, you are still disconnected from any network - just checking the OS and the CPU.
When that's fine, you can conclude that the data coming in from the network was causing a load the OS wasn't handling.
If you can narrow things down, get a
sysdiagnose from a clean start and again when it is "slow" and post a second question with details of what your initial troubleshooting has shown.