The problem with water cooling, and a mistake many inexperienced alternative cooling users make is they forget other components need cooling too. Motherboard engineers and designers engineer critical components (the chipset and voltage regulators come to mind) to be physically located in close proximity to the CPU. The reason for this is so they can take advantage of heat extracting air movement from the CPU fan. Alternative cooling users often mistakenly neglect these critical components.
So when I ask about heat, I am also concerned with heat of the chipset, the graphics card, memory, drives, etc.
And certainly it could be - but remember, you said you installed your old card and it shut down too. So that points back to something else - motherboard, RAM, PSU (new ones can be bad -I still think that drivers are the problem).
Perhaps someone else reading has some ideas but if me, I would remove all unnecessary hardware and attempt to set that motherboard up in a minimal configuration and see what happens - and in your case, I might even try a 3rd graphics card.
One final thought - you said you have a new case, are you 200% certain you did not install any extra case standoffs under that motherboard?



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] followups - though "interesting" is probably not what you were thinking. 
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