Engine and transmission where the back seats used to be, custom-made 2-way remote reservoir coilovers, form-fitting rollcage finished to be hard to notice, and the widest stickiest tires I could fit on the rims.
If you want to get really crazy, replace side and rear glass with lexan, seats with buckets that could be mistaken for factory from outside, and body panels with carbon. Also, a flat floor underpanel can improve aerodynamics with no visible evidence unless you're under the car.