If the valves are out of adjustment you will likely hear it or notice a rough idle, etc. I waited until 2500 miles before I checked my valves and only the upper one was a teeny bit off. If you don't notice any problems, it isn't THAT big of a deal to check it right away.
It is normal to find flakes in the engine oil on the first change, not so much on subsequent changes. The gear oil will be darker next time you change it due to the difference in miles between changes. On your next oil change you can switch to synthetics if you want. I switched at the 600 mile mark to synthetic oils.
Ride safe and enjoy your scooter.