This most likely represents a problem with the hard drive. Get an app like DriveDx that can tell you the SMART status in detail. Unfortunately Apple's SMART support is basically useless in terms of either the data it gives you or the analysis it provides. DriveDx costs around $30 or so but is worth it, IMHO.
If it IS the hard drive, the easiest solution is to buy an external SSD (drive should be around $300 for a 1TB drive, I recommend Samsung 850 EVO, a good USB3 enclosure [that supports UASP for extra speed] should cost you around $20, I recommend Inateck) and run your system off an external SSD.
Hard drives are still the suckiest, most likely to die, least likely to tell you, part of the system :-(
[doublepost=1463456449][/doublepost]I can't speak as to any other changes yet, but it is immediately obvious on older machines (this is a 2007 class machine) that Remote Desktop performance has been DRAMATICALLY improved. Running Remote Desktop to this machine used to use up about 100% of a CPU on that machine (around 50% for the remote desktop work, which I assume was mainly data compression, and around 50% is excess Window Server work). Now it's negligible, less than 20%.
You can even do insane things like watch a movie playing on the remote machine, and the playback is smooth and non-tearing. Damn! It's not EXACTLY the crisp performance of a Sandy Bridge or later machine (which uses h.264 encoding hardware built into the GPU of those chips) but it's as close as you can reasonably expect on a machine that is 9 years old!