I think this might've been covered before...

Drain oil, change filter, add 1.7 L oil (book says 1.9, but mine overflowed once so 1.7 it is), leave bike on sidestand and start it, run for about a minute, then add 0.9 L for a total refill of 2.6 L, and don't bother checking the oil unless the bike has been ridden for a few km. Park on level surface, stop engine, wait a short while (say 30 sec), hold bike vertical and check oil without screwing the dipstick in.

This has been forever the way of oil changes and level checks with oil-in-the-frame Yamahas (including oil-in-the-tank ones like the TTR600), and Hondas for that matter. If you've got the quantity wrong watch out for hot oil spewing out all over the place!

For what it's worth, I only ever check the oil straight after a ride before putting the bike to bed. I've found that any other way leads to inaccuracy and over-filling. After putting a total of 2.6 L in when the oil and filter's changed, I don't check the oil for 1000km or so as I've discovered that the the book value is spot on for my bike.