You can do anything you want with the bike once you get past the 600 mile service. I don't know about the newer ones, but for 1997, checking the valves was one of the most important parts of the 600 mile service.
Ride on the freeway, run the engine to redline, find out what the top speed is, do a few wheelies, act like a hooligan, have fun. 8)
I agree with Bloodshot. I followed my dealers recommendation and stayed under 7000 until I hit 1000 miles. This does not mean you can't get on it though. Definitely give it the gas when accelerating if you feel like it. Loading the engine by either letting off the gas or accelerating heavily is what helps to seat the rings and valves properly.
At my 6000 mile service my valves needed no adjustment whatsover.
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.
One more thing: don't lug the engine, especially in the higher gears. Spinning the motor happily at 5000rpm in 4th will do less harm than thudding the big ends to death doing 3000rpm in top. That goes for after it's run-in aswell.
Thanks Folks . with a 7 mo. old son i don't get to ride just to ride anymore. But I do get to ride to work. Which means about 50 miles of empty freeway ;D(at 10pm) :-[. I did the varing speed thing and kept it under 5500 the 2 times i rode it to work(not exactly my idea of fun). 7500 rpms doesn't sound to bad though. thanks for the advice!