NO.

NO.

Don't worry about the less than a cup of tranny fluid in the cooling system, use the top line.
You MUST pour the new ATF in through the dipstick hole. Get a long, thin neck funnel for that purpose.
The battery tray does not need to be removed. Just pull the air intake duct away from the air cleaner and then back from the radiator to give yourself plenty of room.
The tranny pump is a gravity system, it pumps ATF to the radiator and gravity lets it run back to the tranny. There is no suction on the bottom line.

If the metal clamp is all rusty, get a new one from your local dealer. Otherwise, don't remove it from the hose. Just back the clamp down the hose a little. When putting the hose back on, make sure the clamp is in the same position on the hose as it was originally.

NEVER pump more than 2 quarts out at a time. And, yes, it does take a long time to pour 2 quarts through the funnel :) Patience, the whole flush procedure only takes 30 minutes.

Klaus
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Praying for Cynthia Amendt, heaven bound