I gotta ask, what kind of fluid have you been running in there, and what kind of mix of metals is in your loop? My loops have always been pretty simple, but I've never even flushed a radiator very thoroughly, and have never seen anything even remotely close to that. And my fluid temps are consistently quite high under load.
I had mystic fog go bad and clog up, and then a second hand rad unleased the kraken with some leftover.... something, despite flushes before use.
I got unlucky with second hand hardware, and a bad coolant. Keep in mind that I've also had months of no issues, things went bad with the coolant initially, then bad when I added a second hand 240mm rad to survive summer temps of 43C ambients months later
Sadly, both those events have corroded the blocks, even if just cosmetically - had I known better methods for cleaning the loop initially, this could have been avoided or reduced.
Oh and google says CLR will damage plenty of things, its great for cleaning a rad alone, but eats at some types of plating
Edit: Having a res with 'dead spots' was a big part of my problem - it was designed for liquid entering from the bottom and the pump at the side, where I've got liquid entering from the top and leaving the bottom. Being new to custom water and being second hand missing some of the optional parts, I was unaware that could happen.
The center area of the block has three separate little zones, with a little wall between them. When the fluid gets high enough, they mix - but without liquid entering the sides, those little pockets collected residue and gunk and could never be cleaned by flushing alone. If Alphacool loves me enough, I'm considering asking for one of their helix shaped reservoirs with the UV lighting to really bling up this coolant
