Unless you drained the pan soon after running the engine, some of the fluid from the torque converter would have back flowed. Sometime later, check the fluid level a couple of hours after the engine has been turned ‘off’ and you will see this flow back.
There would not be any problem with filling the sump with the 6 quarts; running the engine until warm; shifting the transmission through the gears; measuring the level; and adding the appropriate amount to bring the level to between the cold and hot level lines. Then take the car out on the road and fill the sump to bring the level up to the hot level.
It should not hurt to use brake cleaner to wash the pan and magnets. Do not use paper towels or clean scrap cloth to wipe the pan clean. You don’t want any lint to remain in the pan. Blow the cleaner clear with compressed air or use lint free wipes if you can find them. Usually the magnet(s) have to be wiped by hand using pinched fingers to pull the beard from the magnet.