It's a pity that Google didn't get you over to MacRumors before you bought 2012.
With that said, 2012 is a much more capable machine.
But myself and many others have benefited from some guys who compiled a new boot.efi file for 1,1 and 2,1.
You replace 2 instances of this file on your main OS install of Yosemite and BANG...IT JUST WORKS.
It does require that you have a newer GPU then shipped with them.
Specifically, the 7300GT, Q4500, AMD X1300, and X1900XT are all left behind by drivers since 10.8.
So, newer GPU and your 2006 can still play with the big boys. You can even switch out the WiFi card and get full ability to run Handoff, etc.
Go to Macrumors forums in the MacPro section, a guy named Hennesie has been running the thread. Nearly 100 pages long, lots of people got it running. Other info at Netkas forum.
Note, it is exactly 1 bazillion times easier if you can use a supported Mac to do the install, then replace the files, then put in 2006.
There is a way to create a Yosemite Installer that works on 2006 by itself but people tend to have more issues with that.
As far as moving your drives, the sleds in 2006 are shorter than 2009-12 so you have to remove the screws and swap them.
EDIT: For the Apple Purists who will doubtlessly come to decry my blasphemy, I have something for you to try. Dig deep in your install, any one since 10.7.5. In the "Core Services" folder is an app called "Expansion Slot Utility". You can try to run it but if you aren't using a 1,1 or 2,1 Mac Pro it won't let you start it up.Now note that this app has not only remained in every iteration of OSX, it has been updated as the OS was. So, an app that ONLY works on 1,1 and 2,1 has not only remained present in EVERY CURRENT COPY OF OSX ON THE PLANET (ie, Jim in Malaysia has it on his MBA) it has been updated. SOMEBODY has to be updating it and testing it.