White crystals in exhaust/cooling system?

I posted this in the 'Common Questions' section three days ago, but did not receive any replies, so reposting here:

I pulled my starboard exhaust riser today to inspect the internal condition of the exhaust hose. Noticed that the inside of both the manifold and the riser is dotted with what looks like little white crystal like deposits. It rubs off easily, so I suspect it is limescale - or is it potentially something more serious?

I recently converted my boat from raw water cooling to fresh water/semi-closed cooling. After noticing the coolant appearing quite rusty, I drained the block and pulled the thermostat today to do a proper flush of the whole system. The lower thermostat housing is also dotted with white specs - looks very much like the same substance in the exhaust manifold and riser, just wet. I can understand limescale deposits in the manifold/riser from brackish raw water evaporating, but the thermostat housing has only ever seen anti-freeze/coolant since I converted the cooling system. How on earth would limescale get in there?

Thanks for any thoughts/advice!

Manifold:


Riser:


Lower thermostat housing: