Red CPU LED

I'm guessing you have the cpu under water and not the sealed H units?  If so, I would re-install the water block and keep it snug but not too tight.  A long shot if you didn't remove it before, but you might want to pop the cpu and check for any bent or burned pins. 

Unplug the rig from wall and hold in the power on button for several seconds to flush the board of stray faults. 

Check all the wires and plugs to the mobo and graphics card.  Especially the smaller ones on bottom right from front panel where power on and reset are in case you bumped something.

Do a system cmos reset.  Check the mobo manual for procedure.  If you don't have a cmos reset button, then there's usually a jumper below the cpu that is moved from pins 1&2 to 2&3, with psu off but plugged in, etc.  Check the manual.  You can also remove the battery for several minutes.

If you have a multi-meter i would check voltages to the 8 pin cpu plug.  Usually black is ground, yellow is 12vdc, red is 5 vdc and orange is 3.3 vdc. 

After that, a blown board or cpu is possible but tough to say from here. 

 

I agree it is a little strange.   Other than checking voltages into the mobo, I don't know of any good way to isolate a cpu from mobo problem in the field.  

The green standby power LED on the bottom is on?   Also , I would try to push in the mem-OK button and hold per the manual to see if anything changes.   Bad memory I don't believe would cause this but ya never know and this does check the memory/cpu controller.    Might get lucky. 

This sounds so much like a pinched wire, somewhere.  Maybe, and not criticizing, it does happen, that a wire is pinched between the frame and rad.    Or a harness is pulled too tight, or kinked.   Try loosening the rads or anything else you worked on , eyeball everything again and hopefully it clears.

Take a real close look at the mobo.  Look for any debris, fluid, etc wedged between components.  Maybe hit the mobo with a blast of air. 

Look behind the mob where the standoffs are for anything stuck there.  

CPU socket and CPU itself looks good. Checked wires and all are good....

I may just bite the bullet and get a new MB and CPU.

I have to agree with Nav.   Like was said earlier, a too tight a mount of the water block or not positioned correctly can simulate a bad cpu.   

Just seems strange all of a sudden.   

Best of luck.