Just did this myself not long ago.
1. You must have a left over gasket for the spin on filter. There should only be rubber gasket on the new filter not on the trans case too.
2. The suction screen filter is a ROYAL PITA! I ended up removing the short hose so I could get it all covered in oil so the whole deal would go back together. I can't imagine trying to do the job in the cold as that hose would probably be a deal buster.
A) The screen has very little for the magnets to pull on. They will all fall together in the bottom after some operation. I know what the manual says, however, Deere is pretty smoked up if they think the mags are going to "stay" that way. Mine were all together on the bottom side of the suction filter when I removed it.
B) I am sure you don't want mags freeballin in your trany so make sure they are down in the suction screen just like they were when you removed them (yes they need to be "inside only").
C) It is sorta spooky putting the deal back together. The suction screen don't want to line up with the cover well (while fighting the bloody hose). That said, if you can't get the cover in place (seated fully) then the suction screen is not in place on the other end (away from the cover). Use caution (and plenty of oil) so you don't
cut the O-rings on the cover.
3. Best I can remember you are correct with your #3 quesiton.
Best regards,
Sean