I have a 2003 Baja, 5 speed, 72K miles. This all started about 2 or 3 years ago. I first thought it had something do with this E10 garbage but I'm starting to wonder if it has something to do with the fuel evaporative system.
Sometimes the car will starting bucking slightly between 2K to 3K RPMs under part throttle. Under full throttle or idle, it runs smooth.
Sometimes this happens if the car has sat for a couple of weeks in my garage at half a tank. Then after about 30 minutes of driving it starts running smooth. As if the fuel being sent back to the tank stirs up any E10/water that might have sank to the bottom.
I tried running the tank down to where the light kicks on in an attempt to get rid of any "bad gas" then topping off with fresh gas but this doesn't seem to do any good.
I also tried topping the last couple of tanks off with pure gas so I'm not sure if E10 really has anything to do with it.
When the bucking is at it's worst is after topping off the fuel tank. Then once I drive the car for about 5 miles, the bucking goes away. Once again, the car idles smooth and runs fine under full throttle. It's part throttle when the bucking occurs.
One day when the bucking was occuring at half a tank, I loosened the fuel cap and drove around. The bucking seemed to have went away. The check engine light that is suppose to remind you that the fuel cap was off never came on!
Also when removing the fuel cap, I never hear a swoosh sound like there is either too much positive or negative pressure.
And the OBD II system is not picking up any codes.
Otherwise the car seems to run fine 95% of the time.