The CPUs are replaceable, so you could replace them as long as you were careful to buy a compatible CPU version that fits the same type of socket. Searching Google should prove a lot of help. I've never done this in your model, but I have replace the ones in my older Mac Pro.
I'm pretty sure the optimal memory configuration is matched pairs, but wouldn't swear to it.
Get 3x8GB anyone using anything that would lead to buying a workstation doesn't mess with less than 12GB RAM is my thinking.
But you don't say what you do or hope to achieve.
W3680 $620 6-core or W3690 are both easy to drop in.
Great articles thank you. I had an older MP 3GHz Quad-Core with factor upgrade to 8 core MacPro1,1 with 8 GB RAM. My motherboard died and the Apple Store I took it to apparently put in the wrong motherboard which caused lots of kernal panics and when Apple finally figured out their mistake, my MP was really in trouble and they gave me a new one (free) - the MP5,1 Quad-Core with 6GB RAM. I asked how that compared to my computer and was told this computer was faster. It isn't. So I wanted to see what I could do to speed it up. From one of the articles you linked, it seems going to more RAM and switching to 1333 vs 1066 was most important.
For my usage, it's not intense. No video production or rendering. I have a tower because I've always had them and like having multiple drives and being able to get under the hood whch you can't do with an iMac.
I use PS, Office, Dreamweaver mostly. What I hope to achieve is no wait states. Example: but not a deal breaker just indication that it's slow, when I open my Applications folder, all the app icons are generic and it takes a few seconds for this to resolve, which I've never seen before. So I just want my Mac to be faster.
then my advice: SSD for system, 1-2TB drives for data, backup etc
the 6 core 3, 33 w/ 16-24GB RAM is popularly known as the sweet spot
isolate OS/apps from data
clean OS if you didn't
cpu MHz still matter and geekbench gives agood impression
cs6 can easily use 24GB if you can and let it, and use dedicated scratch drives