Ok this one has me stumped came here for a little help.
I recently bought a 2000 1500 5.9l pickup for cheap because it need some engine work. Intially it needed a head job, then come to find out the heads were cracked between the exaust and intake valves on every cylinder (common problem with Magnums 98 to 03) So... bought new heads but with the motor having 160k on it i said screw lets pull it and just rebuild the whole thing. Initally the code consistantly showed as misfire on Cylinder 1 when the project began, well now the engine has new cam, crank bearings, and rings, all new gaskets, new heads, and was put back in. We started it up and now no matter what we do the code is misfire on 1,2, and 3 WTF? I know that the current CAT on the truck is bad could it be the back pressure causing the problem? We are going to cut it off anyways but we wanted to get the engine going good first then cut it off.
The injectors are good we are getting spark then motor has been timed... I'm stumped. Crankshaft positioning sensor maybe???? The cam is good. Why would i go from misfire on cylinder 1, then after a rebuild and new heads would it go from that to misfire on 1,2, and 3. I could maybe see 1,3,5 but 1,2,3 uuggggg! Any ideas????

 

you get wires mixed up ??

 

If your cats clogged, this will definitely be the reason why your misfiring. Also, double check the wires like lastrights suggested.

 

The wires have been checked and rechecked. Now what?

 

In your first post you mention nothing about the intake. Did you replace the lower gasket? It's bad(the gasket) if you didn't , which is why the cat is no good to begin with. And why bother troubleshooting any further until the cat is replaced or cut off for now.

 

I'm telling you, Take the cat out and I'm almost sure the misfiring will go away!!!

 

Yeah a bad cat can cause a misfire. Not sure if that's your problem or not but it's worth a shot.

 

so i unpluged the the o2 sensot b4 the cat and still have a miss!!! do you think that it could be the crank or cam sensor?

 

THREE people have told you that the cat could be your problem REPLACE IT!!!!! Unplugging the sensor will not relieve the pressure that your clogged cat is causing.

 

FWIW I've also heard that unscrewing the sensors will releive the pressure enough to know if the cat is clogged... never tried it, but it might work,, just my .02