valve clearances? dont know as i cant speak to your level of ability to set them correctly.

if you think you done good...then move on...
start by opening your shop manual or clymer, and follow procedure for the 3000mi tuneup.
dont get frustrated. shouldnt take you more than a weekend if its your first go (well, unless you find a sht-ton of PO mods). make it fun, not a chore. drink many frosty beverages!

Take your time tho...learn your bike, and check in here for specific questions.
Garbage in = garbage out.
Valves, timing, air, oil, cam chain, carbs.
Clean tank, clean gas, strong battery.
..polish it of w a vacuum sync.