Take out ALL the components you added yourself (aka not factory). SSD, new RAM, etc.
Then reinstall the OS. Make sure that you open up Disk Utility, erase/wipe the entire hard disk (not just a single partition) and then install the OS.
Don't run Migration Assistant, it sometimes can slow down performance even after it finishes migrating.
Go through initial setup and see if anything is amiss. Then slowing add back your RAM one stick at a time. Turn off Mac Pro, add one (1) stick of RAM, turn on, use and see if it anything is different. Repeat with the rest of your RAM.
Then install the SSD, reinstall the OS (be sure to open Disk Utility and erase/wipe your SSD AND hard disk before installing the OS) and then see if anything is different.
You want to isolate the problem, first whether if it's your upgrades (SSD, RAM) or the actual machine itself. If the factory configuration (no SSD or extra RAM) is still presenting the same symptoms, you have a defective machine. Take it to Apple and they will fix it for you. If after adding the SSD or RAM, you find something is really slow or wrong, then send that component back to the place you bought it from for a replacement. And don't do TRIM during this entire process.