I use Valvoline VR1 50W in the crankcase. The high ZDDP (zinc) content in this oil is preferred for flat tappet engines. Any oil with a decent zinc content will do, and since I live in the deep, deep south, straight 50W works great. At 2000-3000 mile oil change intervals, the long life advantages of synthetic don't come into play.
Stock filter is the same as most Ducatis for the past 30 years. I use the K&N 153. The nut welded to the back of the filter makes installation/removal a breeze.
I run Ford ATF in the primary. Manual says to use motor oil, but the ATF works great for two reasons: Its designed to work with friction plates (the guts of an automatic), and being tinted red, I can tell if the primary is leaking, or if the primary is getting fouled by oil from the engine.
I run 90EP in the gearbox, but see no harm in using a multi-weight, such as 85W-140EP. Again, synthetic is a waste of money, IMO, if you plan on changing the gearbox oil on a regular basis (6000 miles or so).