No much done in 3 months of ownership, but the tires is definitly the "easy" mod with the biggest impact on the overall driving experience. FYI I went with the Indy 500 and I love them.
If you can get new tires, lightweight wheels combined with TRD springs is also a good start IMO. It make the car's handling more precise, it's like a scalpel in corners.
The "sound tube" delete might not count as a mod since it doesn't had or replace a part, but it's very easy to do and gives the real sound of the car...not that faky noise.
The worst mod might be a big stupid wing that will give you downforce at 280 km/h.