You're not going to like what I'm about to say.....
You have two most likely scenarios here.
First, run an AHT. (Boot the device holding the "D" key to get to the menu. Some devices on the borderline need opt + D if holding just "D" doesn't work)
If all checks out there... you'll need to wipe and reinstall the OS. It should not take your machine near anything close to 12 hours for an OS install. I just installed a fresh copy of Lion, then Mountain Lion...then Mavericks (before I realized my machine rated for El Capitan)... then El Capitan... on a 2008 15" MBP core duo with 4GB of RAM... and the whole process (because of my goof) took my machine 4 hours.
First of all, make sure that all of your hardware you replaces is rated for your machine. i.e. the SDD, make sure that the RAM clock speed is rated for your machine, etc.
Given that it took so long...and you're getting incredibly slow response times... I would say that either your RAM or SDD is faulty.
Run the AHT. If you get bad results, then you know 100% what to do. If no errors are found... then you'll have to do a fresh install.... then go from there.
I'm sorry. I wish that I had a cooler answer for you.