I just purchased honda civic 2002 vti manual from someone and now confronting with the issue of higher rpms. The car is doing 100kph @ 3200 rpms. I think it should be around 2700 rpms. The clutch is new, timing belt check and timing is correct, plugs are clean and iridium tipped, coils are correct, TPS calibrated to 0.5 to 4.5 wot, engine sounds normal. At low gears torque seems to be ok but near 100 it feels a bit shy to accelerate whereas the rpms are around3200. Valve clearance is also ok.
Not sure about the vacuum things. Although there is not audible sound of any such leak

What else can be the cause