Few comments :
1) regarding your bumpy ride, have you checked the tyre air pressure? Usually when out of dealership, the air pressure is very high. Bring it down to around 260kpa.
2) on the road noise, the factory toyo t1s is really bad in this aspect, performance some more so so and has some chipping issue after some time. After you run down this set, suggest you switch to hankook v12evo2 or flaken fk510.
3) take note on the EFB car battery. Likeliness of it dying within 2 years very high. So monitor with multimeter every month make sure above 12V when cold. If you don't drive long distance/often stuck in traffic jams, suggest you get a lead acid battery charger to perform a monthly maintenance charge. If you can afford it, suggest you get an AGM battery (more expensive, but lasts way longer).
4) istop : well, you'll get used to turning it off everytime you get into the car. It is now 2nd nature to me, not something to be bothered about.
5) for the headlights aim height, see the attachment (although it is for cx3, but since it is similar LED, likely same mechanism for adjustment)
[attachmentid=10207561]
6) the only possible "significant" issue is possible oil leaking on the compressor and the timing tensioner.
7) not sure whether this is fixed, but after some months of driving, you may hear some creaking noise when going over humps on a wet day. If the factory already used revised parts, then this pointer can be ignored.
7 can be fixed by replacing the lower arm. Replaced under warranty. 3 month into, so far so good