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Exhaust Leak Causing Loss of Power

I did find a huge hole in the bend in my stock air intake tube, which I replaced but it still lacks power. I can still hear a slight hiss but I can't tell if it's my air filter sucking up air or a vacuum leak. I didn't plug my old transmission cooler line holes in the radiator, would that cause these symptoms?

Idk if it matters but my CEL flashes sporadically when I'm driving, usually disengaging the clutch triggers it or makes it go away. I feel like the issue is electrical, since that I can't check my codes. If I jump the ECU test with the motor on it SOMETIMES flashes codes. I'm usually not prepared to write the codes down but I managed to pick up on a code ending in "98". The only codes I could find similar to that is "98 and 998 hard fault present".

I'm gonna check that fuel pressure regulator line. Sounds like a possibility that it could have fallen off while I was pulling stuff from the auto tranny out from around the engine. I'm most worried that I unplugged something that can't be reached without taking the top half of the motor off.
 



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The fuel pressure regulator vacuum hose is in good shape. Still getting a "hard fault present code". CEL only works when the engine is on. It starts flashing codes then the motor surges and the flashes stop, so I'm unable to check if I have any other codes. Looks like I need to invest in a real scanner. What kind works with a first gen? Only other things I can think of doing are replace the o2's, plugs/wires and fuel filter/pump to see if that fixes anything.
 






O2 and a tune up would be a good idea, don't think I would worry to much about the fuel pump, normally when they go bad they stop working completely. However, if you do replace it you know you wont have to worry about it going out for awhile.
 






Finally got the codes. I'm getting 998 (O hard fault present), 13 (R rpm not within self test lower limit), 18 (R SPOUT circuit open), 23 (O,R throttle position sensor out of range) in that order.
 






Replaced the TPS and ICM but still having the same problems.
 






I was able to return the sensors I didn't need. The problem is a short in the SPOUT circuit. The temporary fix I used was removing the SPOUT connector until I have time to remove the dash and trace down the short. The result is that the truck runs without stalling or failing to start, but it has a much much weaker throttle response and it idles around 1200-1500 rpms which is annoying.
 






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