Here's the story for me so far..
I have replaced the x-clamps, used no washers underneath or above the board.
...
I also noticed that the board is somewhat bent, and when i look under the board, there is a curve or lump where the CPU and GPU are soldered.
I am currently using the shim method, placed 1 washer underneath the board, 2 washers above the board.
When I boot the console, still shows 3RLOD for about 3 seconds then 2RLOD.
So, was it wrong for me to clean the processors of any residues of thermal compound?

Of course the board was bent if you didn't use any washers! What do you expect? I'd imagine you would need more than 2 washers when using a shim.
When you say you cleaned the thermal compound, you did then replace it didn't you??