Re: Mercury I6 Water Jacket Cleaning after impeller replacement
You can wire-brush the loose deposits on the cover and accessible areas of the block. Vinegar might help, also some of those "purple" spray cleaners that are alkaline-based would probably eat away or at least loosen some of the deposits. The stuff, if left on too long, will also "eat away and loosen" paint and aluminum so just be careful with any chemicals!
Good 'ol mechanical scraping ain't pretty or easy, but usually does the trick. From what I can see in the pic, the block doesn't look too bad and the deposits around the cylinders aren't so much that they'd affect heat transfer.
On the flat gasket-sealing surfaces on block and cover, a gasket scraper does a good job. You could use some gasket-remover spray to loosen them up first, but that stuff also eats up paint so be careful with it.
A razor-blade-type scraper works well for scraping the embedded gaskets, I picked up an inexpensive one at Wal-Mart with replaceable blades, and it does a great job.
Since you have no great love for Permatex No. 3, you might try Permatex/Loctite 518 anaerobic sealer. It only cures where it's squashed by a gasket surface, the rest washes away harmlessly.
Note that most of the new Mercury gaskets have a shiny coating of sealer already sprayed onto them, in your gasket comes like that, you don't really need to use any extra sealer.
The exception to that would be if the machined surfaces at the top of each cylinder are eaten away. Very common to see this, and if so, causes sealing problems.
In that case, the Loctite 518 would work will at filling small gaps. But for larger erosion, try some red Hi-Temp RTV. Just don't use a ton of it, 'cause it will squeeze out and harden. Sometime in the future, chunks of RTV could break off and potentially clog the cooling system.
One last thought, if you're suspicious of more chunks o' rubber in the cooling system, you might try running water up the copper water supply tube (pull the lower unit as necessary), while the back cover is off. It'll move a lot of water thru the motor and you'll get a pretty good idea if you have good circulation. And it might flush any stray bits of impeller that remain.
HTH.........ed