Get the factory service manual first. Do all the normal service work and spend some time riding it around for a while. Fix anything that doesn't work perfectly. Everything will be far easier if you have familiarity and some expertise with your bike before you take it apart to modify it. If something does not work properly after your changes, it will be vastly easier to figure out why if it worked perfectly before hand. It is important to ride it around a while so you can become good enough at riding it to determine what you like and/or dislike about it so you can get that sorted out first. Tires and suspension make a great deal of difference so start there. Don't fool around with rim widths or diameters, or consider swapping the front suspension for something "better". Stick to tires, rear shock(s) and front suspension internals. Very few people know enough to improve on the factory chassis design, and a lot of (if not the majority of) the custom bikes you see may look cool but don't drive as well as the factory intended. If you plan to modify the engine, do that next. Be conservative. Hot rodding your engine for more power comes with a price. It takes skill, experience and time - sometimes a very great deal of each - to get most modified engines to behave as friendly as stock. The factory selects its compromises very carefully to achieve the results that sell. Just be aware that generally alterations trade one thing for another.
Once you have the mechanics of your bike sorted out, you can work on the aesthetics. Of course we all want to do that first, but it's a bad idea. Get your bike to function like you want it to first, and you will know all about the parts that are now off limits for cosmetic changes. You can try different gas tanks and seats and bars and pegs all you want and still have a good motorcycle underneath.
When you are done with all that, and you have the perfect bike, you'll find it a simple matter to take the whole thing apart and powder coat the frame, paint the tank and polish up all the shiny bits. Do things in this order, and you'll end up with an excellent vehicle than not only looks great, but works great as well. If you do the shiny bits first, you'll probably find that they are not so shiny after the whole thing has been apart a hundred times getting all the mechanical parts just right.
