I think you should remove the LSD, and soften up the springs.
Having springs that stiff is never good, especially in GT2 where there is bumpy grass and bumpy roads.
Unfortunately, car with stiff spring rate usually have the best laptime. I learn this from setup vs setup, side by side test, and other laptime comparison. I only use this rule in GT series though, never on other racing game. In GT4 I have bitter experience when someone critisize me for not using stiff spring rate, which should make the car reel the road.
Stiffer spring rate has better grip, this is my personal opinion based on laptime and 1000m test. On GPL, Viper Racing, Nascar Heat, Nascar Racing 2003, LFS, Racer, I would advise to use spring as soft as possible.
Downforce can be used to reduce bouncing on test track. Damper too. I usually want to keep spring rate high.
LSD is personal though. Some people like the stock LSD for R34.
A little offtopic... When I tune R34 GT-R to the max, it gets 774hp, BUT, when it's accelerating, you can see that the tachometer arrow is bouncing from 5000 till 8000 RPM, which doesn't seem to be normal. I spent some time on changing settings, however, that effect disappeared only when I've reduced the power to ~600hp and removed the racing muffler. So, the question is, what is that

And how can I remove it to make my R34 accelerate well.
It happen because the engine flywheel is too light, or something similar. No momentum that hold the rpm to make it steady. What we can do to reduce it is:
- lower the flywheel rating, stock flywheel will give smoother acceleration than racing flywheel.
- do not equip carbon driveshaft.
- and the only thing we can do in race car, use high final drive.
This is the only reason I use this gear bellow for R34:
transmission: move final drive to 5.500 then move auto to 12