Which Toyota/Scion dealership is it? I would suggest seeing how much you can get your Integra sold privately since they might not give you what you want if you trade it in.
Also check the rates between the dealership and your bank. Sometimes the dealership finance is better than most banks and vice versa.
Having your check ready and understanding what your payments and rates are before you walk into the dealership can reduce a lot of the hassle.
You're shit out of luck b/c of the Pure Pricing but make sure the additions that are listed are the stuff that you actually want. I know at Frank Toyota, they don't accept deposits so if there a specific build that you want, they can get it for you. Don't feel compelled to pay for a rear bumper applique and front clear bra if you don't want it.
The hot lava FR-S at KMT has been there for a while and will be if they plan to keep all of that ugly carbon lay and sticker kit.