5 Minute Yosemite Boot Time? My spring 2011 Macbook Pro with 5400 rpm drive takes 5 minutes from pressing the on button to boot. I have about 400 GB of RAW and NEF (Nikon camera) files and only Photoshop and Lightroom installed. It seems to constantly be writing to the HD, and there is a lag time when typing or using drop-down menus. Can anyone offer any suggestions on what might be causing this? I have verified the disk and it found no problems.

I upgraded from Mavericks. Machine originally had Snow Leopard.
I have never done a clean install.
Disk has been verified and found no problems.
All peripherals have been disconnected.

I have not reset the printing system.
WiFi is on.
All login items have not been removed.
FileVault is turned on.

What help steps are next to diagnose the slow performance of this Mac?
Boot in verbose mode to see what is so slow. Then check your backup, actually do a backup before anything else. Failing storage is a likely culprit and slowing io is the bellwether indicator if you get one at all. 

Also, your isolation steps are superb. Remove all accessories, clean install, etc...

lastly, check for io errors in console.app. Verification can show no unrecoverable errors well past the point where rewrite and other mechanisms are compensating for failures in the storage. 

If all that fails, start benchmarking RAM, network and CPU. Process List App

Also, check for swap: High memory usage, macbook pro retina feeling sluggish