There has been many discussions on the tune of a car and whether or not it affects it.
It is also confirmed that Tune A, B, C and D of an integra all can achieve 2:34 on irrohazaka (last stage). So does tuning make any difference? Some may argue yes, some may argue no. Even at the top levels of internet rankings, people have differnt views.
However, having said all that, the things worth changing are carbon fibre elements (like your black bonnet, black side mirrors etc).
There are also discussion that wheels make a difference on wet or dry conditions. Not to offend anyone but i personally dont see any difference. It is the tire and thread patterns on the tire and compound of that tire that makes a difference in real life and in the game, since we are only changing the wheel, there shouldnt be much differnce. As the wheel doesnt come into contact with the surface of the road. But a lighter wheel does improve the performance of your car (in real life) but not sure in the game. However, you might want to try to go for VOLK racing wheels option during parts change should it come up.
So perhaps, just go with the changes that you feel affects your driving positively and makes your car look real cool. and if it doesnt, next time just change back with the parts change option. If you are hitting the top 10 times in the internet rankings, then perhaps tuning may come into effect. If you are within the last 1000 rank, then it probably wont because changing a spoiler or not on your car wont reduce your Akina time from 3:0x to 2:50 seconds.
Hope this has helped.
