Break-in is one of those "black art" things. Everyone has their own way of doing it, but there are a couple of things that seem to hold true for all.
1. The highway is okay, but it is very important to vary the RPMs quite a bit for the first 1000 miles or so. During this time you should literally be accelerating or decellerating with the throttle all the time. BTW, twisty roads are ideal for this. A buddy of mine calls it "jerk riding", cause you look like a jerk. There is a long list of stuff this does for the engine. Again, this an important part of break-in.
2. Oil changes. Don't be scared to change the oil again at 1000 miles. Most of the break-in metal is removed at 600 miles, but it's still a good idea. Machining left-overs in the cases will still be picked up by the oil for awhile too. I change it at 100, 300, 600, and 1000. Anal? Probably, but the engine will make more metal during the first few hunderd miles than at any other time. I also do not use synthetic for break-in, but again that's a preference of mine and a hot potato discussion item.
3. Be reasonable. Give it a chance to get happy before riding it like you stole it. My own personal preference is to use some revs, but sneak up on it. Don't load the engine hard until after 1000 miles, then up it a little at a time until 2000 or so. Is this THE way to do it? Well, it's my way

Opinions vary. But my bike does make 105 rwhp, and Ducati claims 103 with the kit I have (slip-ons, computer, open airbox).
The factory service manual for my S4 doesn't call for a valve adjustment until 10,000 km. I wouldn't believe the 2-valver is different. It couldn't hurt to get it done if you want. By the manual they should have checked the timing belts, battey charge system and changed oil/filter. Additionally they should go through the bike and make sure hardware is still tight. My dealer also sync'd the throttle bodies, although it isn't due until 20,000 km- it was off so it's a good thing.