P0300 Misfire

Trevian26

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I’ve tried reading up on a ton of forums before creating a post of my own but couldn’t find anything that was similar to my problem.
I drive a manual 2006 Mustang GT with stock tune.
It has a CAI, UD pulley, new spark plugs, factory coil packs, factory injectors, sub/amp, don't know the specifics but a bigger battery than factory, and I only pump 93.

I recently had a code thrown up for a cylinder 1 misfire and decided to replace all my Sparkplugs as they seemed to be in bad shape with motorcraft. Code went away but then had my bank 1 sensor 1 02 sensor code pop up. Having both banks sensor 1 get replaced this weekend as I couldn’t do it myself since the cable sits on top of the transmission. But other than that it drove perfectly fine for about a week until yesterday. I installed the UD pulley and did a test drive after, going speed limits. Decided to just run my scanner just cause and to my surprise, I have a P0300 but sometimes it says cylinder 6, 3, and 5 are misfiring as well. Looking at the live numbers while driving it seems cylinder 6 is taking the most beating. Another drive around the block, I noticed my CEL would flash when I shifted to 3rd gear putting me at 2100ish rpms. Once I slowed down and was returning home the light stopped flashing and my scanner was only readying a misfire code for cylinder 6. I am not sure if the UD pulley had anything to do with the issue but I’m looking for further insight on troubleshooting this issue.
 

JC SSP

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Have you checked your electrical charging system (batter, alternator, cables, etc.)
 

86GT351

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Have you checked your electrical charging system (batter, alternator, cables, etc.)
This. Also could be the Intake Manifold. Not uncommon for the runner controls to go bad. What pulley is on the car? I have seen that over the years that if it is not properly installed it can create a random misfire.
 

Trevian26

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This. Also could be the Intake Manifold. Not uncommon for the runner controls to go bad. What pulley is on the car? I have seen that over the years that if it is not properly installed it can create a random misfire.
I installed an SR performance UD pulley yesterday.
 

Trevian26

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Did the light come on afterwards?
The CEL never officially stayed on, this morning when leaving for work it started flashing for about 10sec as my RPM was increasing and I could feel the loss in power and it jerking and since I was in a hurry just turned it back around about .3 of a mile and drove my truck instead. As for my test drive yesterday after my install, nothing came up at all but when I was looking at the live data driving around I was seeing random misfires then got a P0300 code but no CEL officially.
 

86GT351

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The CEL never officially stayed on, this morning when leaving for work it started flashing for about 10sec as my RPM was increasing and I could feel the loss in power and it jerking and since I was in a hurry just turned it back around about .3 of a mile and drove my truck instead. As for my test drive yesterday after my install, nothing came up at all but when I was looking at the live data driving around I was seeing random misfires then got a P0300 code but no CEL officially.
OK. But was the light an issue before you did the balancer/pulley?
 

Trevian26

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OK. But was the light an issue before you did the balancer/pulley?
A few weeks back the CEL came on for a p0301, I changed the spark plugs and cleared the code and it ran perfectly fine after. From then until yesterday no light.
 
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