I think limiting the engine to 5,000 is being over-cautious. The book recommends no more than 5,500 - 6,000 in the first 1,000km (600miles). It's difficult if you go only to 5,000rpm, since the engine doesn't really even feel smooth until you're at 4,000 rpm. Laboring the engine at low rpm can't be any good for the engine either, so you have to strike a balance. The 1,000 rpm range is too narrow; it would make the bike pretty tedious to ride.
I went no more than 5,500 for about 200 miles, then up to 6 every now and then for the rest of the first 600 miles. Full run-in, according to the manual, is 2500km. At 1,200 miles, I'm almost there so I've touched 7,500rpm briefly from time to time.
You're gonna love it when it's more run in and you can start to twist the throttle again. It pulls like a train. OK, it's not a 999, but it's still plenty of fun for the street. CHARGE!!!
As for tightness of bolts etc, I love the way Ducati marks most of them with fluorescent green paint. It's easy to see if any bolts have worked their way out.