You would be better off doing it in the original factory colors. If you customize it, it is not a true restoration and it will take away from the value to a serious collector.
Whatever you do, you will never get the $$$ from your labor out of it that you have put into it. So you are not going to make any profit by restoring it on the vintage/classic/evo market unless it is a full on concourse restoration or a very rare bike, and then that is if you can find someone who truely has to have it. If you were keeping it for yourself then the bike is well worth your time.
Hope this helps