Gasket - don't need anything on the gasket. Make sure the mating material is clean and dry - no need to silicone or RTV. Some people still want to put it on, but that flange is very thin - be way too easy to accidentally get RTV or other sealant pushed into the transaxle - then you'll have a bigger problem on your hands. On some gaskets - there are holes in the corner that are slightly smaller in diameter than the others. This is so you can thread screws through those smaller holes to help hold the gasket to the pan and get them started on the bottom of the transaxle.
When tightening the bolts on the bottom of the pan - tighten them in stages, evenly tighten them, so as to not distort the pan flange and make sure the gasket is not pinched or damaged. Inspect the bolts, might have thread-locking compound on them from the factory (looks like red or blue colored paint on the threads). If there are present - you have to add thread-lock before reassembling the pan.
Filter - should be three screws (just note their positions, as the screws are of different lengths) - there is usually a paper or cork gasket that seals the filter to the pump assembly.
I've seen replacement filters that have a metal screen, fiberous mat, and some that were like of felt or foam materials. OEM can be any one of those, depending on where the car was manufactured.
Magnets should not have moved from their original position - just replace them where you found them. But there are very visible raised portions on the bottom that outline where the magnets go. Once you clean the bottom of the pan, you should be able to find them very easily.