Actually, you'll get about 3-1/2 if you pull the plug. The threaded part does protrude upwards into the pan, so it will retain some. You'll get the full 4 quarts if you pull the pan - or you can top off with four quarts, and start the "four-quart" cycle from there (that's what I do most times.)
It's not generally necessary to drop the pan. I'll do it the first time to check everything and clean the magnet in the pan, and then I'll probably drop it every third or fourth after that for the same reason. The "filter" is little more than a sump strainer, and if you find crap in there, you probably have larger problems.
I usually use a cork gasket (it's what I get, and they work rather well) with a little RTV Black on both sides to finish sealing. Clean the pan edges and mating surface on the case with Scotch-Brite pads to remove residue.
I have found that using about four studs (one on each corner) helps immensely when getting everything lined up and started - they're M6-1.0x25m/m, if you have a local source for them.
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