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Ok, I have already done the auto to manual swap on a 01 EX, I also have a SF Kit...I am having problems with the car lagging when the accelerator is pushed in. It hops and lags in btw shifting and laggs in neutral when you hit the gas like there is a "hole" in the accelerator. I have talked to Honda and they thought it was the tps, well I replaced the whole throttle body (idle control valve, tps sensor, and actual throttle body) with a brand new one for an manual tranny (yes they are different). I have also replaced the following:
Tranny
Spec Stage I racing clutch and 6 lb flywheel
shifter
shift linkage
slave cylinder
pedals
clutch line
master cylinder
ecu
engine wiring harness
tps sensor
idle control valve
throttle body assembly
If anyone knows what could be causing my problem please let me know. Just some extra info, I noticed on my friends 01 factory manual civ ex that his map sensor is right on the intake manifold, mine has a spacer set in btw it and the intake manual from the factory, would this matter at all?
thanks for any info!!

 
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Well one problem I see is your flywheel. Way too light for the horsepower your pushin

 
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Would that cause a lag in the shifting though?, it is almost like it is not getting fuel at the precise moment, that is why everyone that it was the tps not sensing the throttle being open.

 
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well if ur flywheel is too light, it could cause ur rpms to rise and fall fast, but try tightening ur accelerator cable, it might be loose, or maybe u might have a fuel problem, clogged injectors and what not, try some injector cleaner for the fuel, i recommend lucas fuel injector cleaner from autozone, real good stuff