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Hey guys I'm pretty lost was wondering if anyone could help, all info is appreciated! So here's the situation, I just swapped in a l67+4t65hd into a 2001 se. The problem is the motor will not run right, I did tune the pcm to a supercharged file. It has a random misfire that I can not get rid of for the life of me! I changed the ignition packs, the wires, checked spark plugs, checked all my grounds, made sure the injectors were clean, fixed the egr leak, case relearn and some other things I can't remember. What's funny is the car will sometimes run real *shoot*, but then clear up and run like a champ! Not sure how it can run good then run bad and vise versa. Sorry for the long read and thanks for the input!

Ignition control module? MAF sensor?

Does it throw a P0300? If not, consider the crank position sensor as well.

Yes it is saying random misfire in my dtcs and the ses light will come on and fill flash. I will check the icm, maf is cracked a little but when unplugged it does make the motor run worse. Funny thing is after doing the case relearn or flashing the pcm seems to make the car run better even if I shut the car off and start it right back up, but if the car sits for an hour or so it'll go back to run bad again?

Does it run bad at idle? If so you can test the injector pulse with a 194 style bulb. Bend the tabs straight and you can plug it into the injector plug, with the engine running the bulb will flash with the injector pulse. This at least will tell you if the injectors are getting the signal to fire.

Runs bad at an idle and put in reverse its even worse and even in drive it'll run bad very hesitant and shaky with no power but sometimes will clear up and idle fine and run good at wot. I know I'm getting fuel maybe to much I can smell it? I will definetly check them though with the light thanks for that tip!

Also I forgot to add it has a very hard time trying to start sometimes and has backfired on me a couple times

It sounds like you have the plugs wired in the wrong order. This is easy to screw up. Make sure you didn't.

I'm with Bugsi. Sounds like a firing order problem. Also double check that you got all those motor and trans grounds in tight and clean..a loose\ dirty ground can make a waste spark system go all kinds of squrrely.

I really wish it were the firing order but I have checked a million times to make sure its right and it is. There's something going on with my spark timing, and no matter what I do I get random misfire sometimes it'll show up sometimes it wont. I've done everything to the car and no matter what I do I cant get it to run 100%. I did have the timing set at 40° all the time and that seemed to make the car run alot better than what it was. Not sure where to go anymore.

I know some guys have had problems with the o2 sensor arcing over to the wires. Look it up on the search. If you reroute the wire in the back away from the sensor maybe that will help. Probably a long shot but it's worth trying if it helps.