Oil Level

Don't know how much you know about these bikes but you are aware that it's a dry sump engine so draining is not per your average wet sump bike ?

If 1.5 litres came out and the oil level was fine before draining, then logic would say putting 3 litres back in has vastly overfilled the bike. If you use it like that the excess will likely get pushed up the crankcase breather and into your air box. Always go by the oil level and not quantity alone when refilling as you will never remove 100% of the old oil in a simple oil change. There will be pockets of oil trapped all over the engine.

Checking the level after refilling is a different method as well due to the dry sump. Engine has to run for a warm up period and then turn off and allow the oil to track back to the tank for a few mins, then look at the level. Your just getting it ballpark at first fill (about 3.7 litres with a filter change) and then top up after it has run. By the way, if you left lots of dirty oil in via only partial draining then your new oil has mixed with it and is now contaminated.

where did you drain the oil from, which drain plug did you remove ?

There is a second magnetic drain plug just behind the oil filter on the crankcase which should be removed as well. Having said that I can't believe there would be anything like another 2 + litres in there. If it were me I would completely drain the oil (from both plugs) and refill to correct level.

You won't get 4 litres in there because things like cam chain tensioners are captive (like a cup) so oil gets trapped inside them. There will be lots of trap points that will contain oil that won't drain fully no matter how long u wait. If you get more than 3.5 litres in there from a full drain with an already oil soaked oil filter I would be surprised.

Depends how badly it sticks, it's not unusual to get light rubbing even if everything is fine. Ideally you would want new pads because the old ones will have worn to match the face of the old discs but given the limited time you might have to go with it as is. Check the disc bobbins are free or the disc might not be floating properly. Push a suitable size flat blade screwdriver or similar head into them till it grips and twist. If they don't rotate freely, squirt a little lube on them (protect the braking surface) and repeat until they are free.