5 Minute Yosemite Boot Time?
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