I ended up getting frustrated so I brought it into the Apple Store (I have applecare on this machine). Just a black screen with an Apple logo which would sit there. Anyway, boot times would take an hour plus some days, and sometimes the system wouldn't even boot at all. I manually back up my files to my backup server, and then restore my files manually, making sure I do not carry over any of my preference files. I should note, that I never restore from Time Machine backups. I was reinstalling OS X every week (once every two months prior), as the first two days after the install were the only days that it would run correctly. In December 2015, my system was unusable. Because of this, I stopped using VM's (I was also given a work laptop so I could stop using my iMac). I could click the Safari icon, and then get lunch before it would be open. The host OS during this boot time, is completely unusable. If I even open a virtual machine now, what took 15-30 seconds to boot now takes upwards to 20-25 minutes. Once I installed Yosemite, everything went downhill.

I had no speed issues, I was able to use both the VM and the host OS. Prior to installing OS 10.10, VM's worked incredibly well. I work(ed) a lot with Virtual Machines, as I build and test software on different platforms.

Side question - I know the serial number and MAC addresses of the WLAN/Bluetooth & Logic Board's can be changed using Apple's utilities, but I thought that disk drives weren't? I have never seen a utility to replace a drive serial number (and I replace disk drives in server nodes and raid arrays on a daily basis). that's what I was told, at least - I question it because my HDD's serial number never changed, but it was explicitly written on the work order that the drive was changed). I have brought it into an Apple Store, who has replaced the logic board, the bluetooth/wifi card, and the hard drive (well. I purchased it in January of 2014, and ever since day 1, it's been a nightmare. I have been experiencing so many issues with my Late 2013 iMac (14,3 - 21.5' 2.9GHz, 8GB DDR3, 1TB HDD, Nvidia Graphics).

Used late 2013 imac