Only you know what will make you happy... But I would start with the basics and work up.
First, better suspension. Get a set of quality coil-overs. The Tokicos are not track worthy, they are an OK street shock - hint, stay away from any adjustable shock that combines compression and rebound adjustments, you will never get the damping curve where you want it. Stick with rebound adjustable shocks unless you really know what you are doing, you can really screw up a car playing with the compression settings.
Swaybars: if you get the springs and shocks right you wont need to bolt a 15lb weight to your rear axle.
Brakes: the stock brakes are overkill for the weight of the Yaris. Upgrade the front pads and leave the rest alone. If your car has a lot of miles, or the lines look suspect, get the stainless ones. We only added brake cooling ducts when we went to the 13" wheels because the airflow is so restricted, we have still never had fade - and this is with a 40min race, not a few hot laps.
Trans: this makes the car, you must get an LSD. If you have the money get the OS Giken, if you want to go cheaper get the TRD unit. BUT while you are in there install the xB 4.312 final drive, it really wakes the car up. You will already be paying the labor (or doing the work) to pull the stock gears when you install the LSD, it is not much more work to swap the gears.
Tires/wheels: 13" wheels make the car a rocket. They give you an even shorter final drive, lower the cg (and help get the roof down out of the air), they are also a lot lighter than the big stuff. Another advantage is you can run a wide 13" tire without it bashing the fenders, no need to cut or roll.
Bolt-ons: Get the header, intake and ecu. You can really unlock some power.
That alone should be enough to take out any stockish Cooper S. If you are not satisfied at that point you have all the basics covered, and now you add the FI.
As far as a radiator, the Mishimoto xB unit pretty much drops right in (you have to drill two holes in the core support), and we used the xB hose set.