I just kind of went through this about 8 months ago.
If I had to do it all over again with a stock bike...best mods to date:
- Braided front and rear brake lines as well as EBC HH pads and some high performance fluid - ~$200
- Re-spring the front forks to your proper weight and good fluid - ~$120 plus someone to help you change them
- New windscreen (double bubble or otherwise to protect better) - ~$60
- HID headlight setup (you would NOT believe the difference, especially if you ride at night) - ~$180
- 43T rear sprocket and ZZZ 530 chain (however you COULD do a 16T front and use stock chain) - ~$180
- Speedo-healer (everyone forgets to mention this when you start messing with gearing) - ~$80
Very first mods done should be to better the brakes and get the suspension set properly...after that, my personal preference would be HID, then the sprocket, speedo healer...THEN look at NOS, pipe and power commander, etc.