You can use either a 4,1 or 5,1 tray, once you flash your 4,1 to 5,1, a three minute job. Look
here. 5,1 will also allow use of 1333MHz memory in contrast to the 1066MHz a stock 2009 uses, but the speed gain is far less than the numbers suggest, and generally not worth the expense.
Cost? You are being quoted $2,550 US - all amounts here are in US $ for comparability. Used X5680 CPUs (3.33GHz, 6-core) sell for $1,700 each new
here, which is a lot more for two plus a processor tray with heat sinks than you are being quoted. On the other hand, used X5680 CPUs routinely sell on eBay here for $700 each. A used dual processor tray with heat sinks can be had for $300-600, but they do not turn up often.
The X5680 is 10% faster than the fastest 12-core that Apple sells here or in Australia, which is the 3.06GHz X5675.
Upgrading CPUs on a dual core 2009 is far from trivial. Unlike any other 2009-2012 Mac Pro, 4- or -8-core, the 2009 used a CPU design without the Integrated Heat Spreader, the alloy plate on top, and without a sprung retaining clamp. This makes the CPU 2mm thinner than any other and installing a regular IHS CPU dictates that you adjust for the thickness when torquing the heat sink, or you will destroy the fragile CPU sockets on the processor board like
this. A replacement dual processor board will cost you $300-400. If upgrading a 2009 dual processor board you will also need to add thermal pads on top of the voltage regulators and amend the temperature sensor connectors in the base of the heat sinks to ensure they maintain proper contact with the backplane board.
DIY upgrading of any other 2009-2012 model, 4-core or 8-core, is far easier and lower risk as all use the IHS design, identical in dimensions to the one currently in your 4-core machine.
Do you need the additional speed on moving from a 3.33GHz 4-core to the 12-core? That's a function of what you use your Mac Pro for. If heavy CPU applications are your primary use then the difference will be very noticeable. You can objectively measure this by running Geekbench 64 (a few $) on your machine. GB measures CPU and memory speed. I would expect it to return around 11,900 with the 4-core W3580 3.33GHz CPU you are currently using. By contrast, the X5680 pair will Geekench around 23,900, or more than twice as fast. A large difference.
Does it make sense to stick with a single CPU machine, upgrading your 4-core W3580 to a 6-core W3680 ($574 new
here or $550 used - no bargain that)? The 6-core returns around
16,000 in a 2010 compared with around 12,000 for your current rig - a 25% CPU speed gain. Probably not worth the expense.
On the other hand, if more graphics intensive applications are your primary interest, then an upgraded graphics card may better address your need for speed.
Conclusion: If the part offered you is really new and if you need the doubled CPU speed, then it's a bargain. But you can pay far less using used parts if you can handle the DIY and related IHS risks with a 2009 dual-processor tray. If your need is primarily GPU speed then it's not a good investment, get a better GPU. A GTX 780 runs $650 here in a stock PC version. You will lose the Apple start-up screen and the spinning cog - blank screen until you get to the login display. Other than that it works fine. Get one with twin 6-pin sockets running cables
like this and connect the other ends to the sockets on the backplane board in your Mac.
The title for your post is misleading - you need to change 'Fan' to 'CPU' to get the right readership.
