I have a 2005 Honda Accord EX 2.4L Automatic transmission with 253,000 miles with an intermittent flashing MIL. The code its throwing is P0301: cylinder 1 misfire (pending). I've changed all my coils, plugs, and even 2 injectors. My compression readings are as follows:
cylinder 1: 170
cylinder 2: 165
​​​​cylinder 3: 155
cylinder 4: 170
The MIL flashes when im going over 40 and my RPMs are over 3500. My car will not upshift past 3rd gear even on a level road.

However. As of today I realized when I turn off my "cruise control main" button on my steering wheel off EVERYTHING goes back to normal. No misfire codes and absolutely no problems getting up to speed or shifting. I was able to drive a whole 6 miles with absolutely no problems. Any idea what could be going on?

 

This is difficult, because the cruise control and engine performance shouldn't be related. I think the 05 accord throttle was the last year with a throttle cable attaching the gas pedal to the throttle plate, but I'm not 100% sure. Newer accords have drive by wire, where the PCM controls the throttle plate. See if the throttle body has throttle cables attached.

I'm wondering if the cruise control is trying to set the speed on the throttle body even if you don't have the cruise set to a certain speed?

Do the symptoms return when you turn on the main cruise control power switch?

 

I honestly scared to turn the cruise control main back on. I'm worried about a short as my car did have a leak from the top of the roof before I got it that I fixed that that I should have mentioned before.
on the other hand I did drive over 30 miles today under heavy load and it did great, no codes. So I'm pretty sure the problem is isolated to somewhere to the cruise control main switch or control unit maybe? Or like you said the throttle body cables have come unattached. I'll go outside and check right now about the throttle cables.

 

yes the throttle cables are attached.

 

Where was the water leaking into the car? Front vs back? Driver's vs passenger side?

 

front of the car, all along the front from along the windshield. It was rusted along the line where the windshield meets metal, and would leak along there.

 

The cruise control unit is under the driver's dash. You may want to unplug the electrical connector and look for any signs of corrosion on the electrical connector. Also look around the fuse box area for some grounds that could be corroded from the leak. I believe they are somewhere above the fuse box.