Kong:
1) Congrats on picking up a bike. A 550 isn't a sportbike by today's standards, but compared to your Harley it'll feel like one if it's built and set up correctly. It's true that a 750 could have been a better choice in terms of meeting your power goals, but the 550 is so much better-looking that I commend you on your choice. Hey, us 550 guys gotta stick together!

2) Don't let the haters get to you. I have to admit that I've never seen Harley guys and supersport guys lumped together until reading this thread! As a sportbike guy I'm a bit offended.

3) $3k is NOT a big budget for building a nice cafe anymore than it would be for building a nice Harley. Other than the purchase price of the bike itself, I don't see how a Honda cafe would be any cheaper than a Harley. Stuff like rims, spokes, brakes, fabrication, paint, wiring, lights, upholstery, custom bodywork, exhaust, etc. aren't really brand-specific and the really good stuff costs, period. And anything related to the motor you're buying 4 instead of 2.
4) If handling & suspension is your biggest concern, then plan on some good shocks in the back, and new springs, RaceTech cartridge emulators, and a fork brace in the front as a bare minimum. Swapping the front end to something more modern will yield better results if and only if it's set up correctly, but that's more money and it changes the look more, so you have to decide if that works with your plans/goals or not. Hang out in the racing/performance section and find out what the racers do to get 550's to handle.
Good luck and keep us posted on your build!!!