My question would be ...why was the head removed?

It's best to run a compression test before pulling off the head....
and Look at the plugs to see if 2 of the four next to each other look different from the other two.
but............
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Use a rag to get the water out of the piston part of the cylinders,
and oil them down with WD40.

Scrub Out the Rust.......
Get a stiff gun-cleaning brush that can be pushed down into the
water jaclet holes of the sleeves to scrub loose the rust/scale/chunks from inside the block water jacket.

Lay a straight edge across opposite corners of the block, as well as straight across side to side of the block to be sure the block is not warped.

Look at the plugs to see if 2 of the four plugs next to each other look different from the other two.

Drain dirty water.....
Find the block drain screw, drain the dirty water and spray clean water into the top of the water jacket holes of the sleeves. Once the engine is back together, pour some radiator cleaner into the radiator, top up with water and run it for at least an hour after it warms up....take a trip....then drain all the water out of hoses, drain screw and block, and keep running fresh clean water through the system until all water looks clear. Drain ALL water and add coolant.

Install a new head gasket. Toss out the old one.

Does "bottom end" mean the oil pan?-Bob