I'm on the other side of the process right now (reassembly) and if you take some good notes, keep things organized and take lots of pictures you should have no problem with this bike. TW's are very simple motorcycles. As far as needing to replace anything there isn't much during the process that can't be reused. Just a couple things to watch:
- Steering Head: When you get this apart balls from the bearings may fall out. I personally didn't care because I plan to swap to an ABR roller bearing kit.
- Swing Arm: There are bushings inside the swing arm pivot that can easily be lost or damaged. The rubber portions may get destroyed if you try to pull them out for powder coating.
- Air Box: Easiest to pull it out when the sub-frame and swingarm are removed.
- Engine: Typical replacement parts as needed (gaskets on the intake and exhaust side as required) Also, if you plan on changing the front sprocket you will need a new left side engine cover gasket. For reasons I can't explain yamaha decided not to have a separate cover for the sprocket.
If you are going to rebuild the front forks you may want to loosen the top bolt while they are still clamped in the triple tree.
Good luck with your project!