I don't have a clue about the red leds. Are they on the GPU itself?
When you turn on a comp, the power supply sends a signal to the motherboard...if everything on the motherboard is in order, the motherboard sends a signal back to the power supply to turn everything on. This is called the POST test.
It stands for Power On Self Test.
It seems you are passing the POST test or the computer wouldn't boot at all.
Things about the GPU that may be causing the issue.
Sometimes if we tighten the screw on the rear of the GPU too tight, it makes the front of the GPU raise a bit and break some contacts. I've seen comps boot slow because of this, or not boot at all, or boot but with no display.
You might want to make sure the GPU is seated firmly in the slot. You might also make sure the RAM sticks are BOTH seated firmly in their slots.
Like I said before you might have released the pressure on the CPU heatsink just enough to break the seal made by the thermal compound. It may turn out that you have to remove the CPU cooler, clean off the old paste and put new paste on the CPU.
If the temp goes up too fast on the CPU, that could slow or prevent the comp from booting.
The other thing that can slow a boot, is if the drives are not plugged into the same connectors that they were before. This can confuse Windows itself.
You can check in Disk Management to see if they are still set up like before.
Here are the no fun possibilities...
GPU is dying.
Motherboard is dying.
When you took out the motherboard with the CPU cooler attached (which you should never do with a large CPU cooler) you may have "flexed" the motherboard. This can cause microscopic cracks in the tiny circuit runs on the motherboard.
Sometime this will kill the motherboard, sometimes it will slow things down.
For now, try this...it may point to something. I doubt it, but it doesn't hurt to check...
Get SPECCY here: http://www.piriform.com/speccy/download ...get the
FREE version from the:
Piriform Link ...Speccy is a really nice system hardware/temperature, information Utility.
...simply install it...and run the program...then post a screen shot of the main page of the program, when posting a problem/question on these forums.