I'm willing to bet that the machine was stored on its side and not used for a while which then resulted in either a failing of only partially working pump for CPU A. If anything, disabling that CPU and running it a s a dual 2.5 would make it so that you could still use the machine.
That's what I'm actually doing right now with CPU B disabled and the CPUs running in reduced power mode. I don't know how to disable CPUA since I think that's the default CPU though.
As far as a test to check the pumps I don't know. I have a question for you though, do you see any evidence of cracks in the tubes? I know just from dealing with any issues from any system that requires liquid cooling that the tubes can crack from either decreased use or over exposure to the environment due to improper storage.
And I wanted to say that the thread you read (which is awesome) also shows what you probably shouldn't do when it comes to altering the hardware designed and used for Apple's machines. What the OP did was creative, but it is also very possible that he was just using his Quad for too long with too much demand that caused his computer to eventually fail. I'm pretty sure there have been quite a few G5s and Mac Pros from Disney that have bad CPUs due to the high demand put on them.
Not to say that it's not worth saving, but having a machine running hard for 10 years is awesome in itself.