Quick answer since I have a 2002 as well (DE03):
1 - Swap expansion chamber (the blobby exhaust bit) to an Athena or something. This was the big thing.
2 - Pull out the reed switch from behind the speedometer. Do not disconnect it or cut any wires, just wrap it in tape and stuff it aside. It detects when the needle gets to ca 80 km/h and cuts ignition there.
That should be it, your bike should now rev freely to 9500 rpm and do 120+ km/h.
Also: ensure that the YPVS is working as it should. Remove the round cap on the left side and turn on ignition. It should rotate back and forth a little, then settle such that the groove on top is right over the hole.
Explanation on that last bit: The YPVS switches the port timing between low revs (more torque) and high revs (more power) as the revs increase and decrease. Variable valve timing, you could say.
When you turn on the ignition it rotates back and forth (flips between low and high mode) to scrape off soot. The resting position should be over the hole because they used that hole to fixate the valve in low-revs mode (and turning off or removing the solenoid actuating it) when they restricted bikes, but I believe they stopped using that method after 1998 or something. If it does not rotate back and forth with an audible "bzzt-bzzt" when ignition turns on, your YPVS is not working and stuck in either of the modes.
As for the inlet manifold I did a thorough CFD analysis and found that you cannot improve it. Leave the plastic bottle on, it smoothens out the gas flow. The carburetor should not need anything either, it is likely a Mikuni TM28SS with a 240 µm main jet, which is perfect.