You are really getting in to the new bike.
I was the same when i got my '04 model.
Although i didn't strip mine down like you have

As others have said, looks like the previous owner wasn't a vert mechanical fella, or knew much about looking after things.
And considering, its only travelled so little k's in 2 years.
I'd be checking the Battery (and buying yourself a tender)
Replacing all fluids, engine oil, brake, clutch, radiator, the lot.
Check the Clutch Slave for leaks and gunk build up
Check the Bottom Swing Arm Linkage Bearing
Look in the Carbs to see if the Restrictors have been removed (images on this site http://www.billzilla.org/mybike.html )
Checking and Setting up the suspension from the previous owner (mine came so bad, i have no idea how anyone rode it)
Check if you have a rear shock shim fitted
Take off the right hand side Can and have a look into the header Y peace ;)
Buy her some some new tyres
And just go riding
