If you could, just test fit the front and rear bumpers yourself. If you're happy with the way that they fit, just ask the shop to install the side skirts to your car. I'm sure that they'll charge you considerably less than 400.

As for the Feel's fenders, the copies that weren't intended for the EK's yes the front flares are whole fender replacements and the back is just the flare itself. But since you have a 99, you might have the option of just getting the flare for the front as well. If you do plan on getting the Feel's, might I suggest that you wait until you get those before you ask for a shop to install the body kit. It'd be cheaper that way.