I also upgraded my Mac Pro 2009: CPU, video card, WiFi/Bluetooth, memory, SSD... It takes some time to find the best options. I advice not to upgrade everything at once. Just part after part and read the topics in this forum.
For the WiFi/Bluetooth I chose for OSXWifi.com's solution and it works great. You replace the internal cards and cables and you get the latest version of WiFi and Bluetooth without installing drivers.
I added a Samsung 850 pro with an OWC Mount Pro 2.5 in bay 1. I use it only to run my system and applications. I moved my user folder to on an other larger disk in bay 2. In bay 3 I have a backup disk.
The next upgrade will be the Sonnet Tempo SSD Pro Plus + another Samsung 850 pro SSD.
I now have the new Magic Mouse 2 for a few hours and it is much much smoother. With the older Magic Mouse I had sometimes lag problems because of the thickness of the Mac Pro case.