My CRX did something similar with the throttle; pulling up on the pedal would get the RPMs back down again. I pulled off the intake and hosed the inside of the throttle body with carb cleaner and wiped it out with a rag. Had to do that several times before the rag came out without a bunch of gunk on it. The throttle closed just fine after that!
With a four-speed, I think your car is probably the base or "DX" model, with DPFI (Dual-Point Fuel Injection, a throttle-body injection setup) instead of MPFI (Multi-Point Fuel Inejction, a standard port injection setup). Anecdotally, an MPFI swap gains a bit of power and fuel economy for the DPFI cars. But it is some work.
The MPGuino is an Arduino-based MPG meter. You solder the board together, plug it into your desktop or laptop computer, and load in the MPG program. Then you hook it into power, ground, the VSS (Vehicle Speed Sensor; inside the speedometer of that generation of Civic) and fuel injector wires.
-soD
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