I don't know about paint, but changing the headlights would be tough. You'd have to get the race fairing and cut the shapes our yourself. Since the front is so skinny, it might look weird. Not to mention finding headlights in the right shape that would fit.
The rear is nice, but I preferred the way I did mine. I did away with the rear plastic completely and put the blinkers in the 2 square lights on either side of the brake light. I popped out the small piece of plastic under the brake light and replaced it with clear plastic, so the light would shine on the license plate (a requirement in CA). I also mounted the license plate with 2 L brackets under the brake light. There are 2 fairing bolts there that worked perfect. That cleaned the rear up real nice.
Lowering the bike... I don't recommend it. It messes with the ergonomics/performance of the bike. If you need it to be lower for footing, get a spare seat and shave some of the foam out of it where your ass normally would be. That'll give you about an extra inch worth of reach.
Unless the flames have clearcoat over them, they should just be stickers you can peal off.
If you feel like you've outgrown your 250, you've probably outgrown your helmet too.