please help!!! 2000gt 3,4,7,8 misfire/dead holes!!

hi ok so here we go, i have a 2000 gt mustang i picked up off a kid that ran perfect excepte for the fact that it stoped oiling to the passenger head, i pull out the motor and dropped in a new 04 gt romeo motor with 30,000 on it and it was clean!!! after getting it in and using the old wiriing harness, i fired it up and it ran like ****! i checked and numbers 3,4, and 8 were not hitting. so i replaced all the plugs and three coil packs now its missing on the same plus 7!?!?!? the front 4 are hitting but the back 4 are not. the only thing i did different was the car had two o2 like plugs for the back two sensors and i didnt put them back on just left them un plugged. i checked all the coils and there good, i'm pretty sure i checked the alternator right and its charging so plus i hooked up the battery charger and put it on jump mode to make sure it was getting enough fire so its not that. some of the plugs were wet when i pulled them back out so im pretty sure its not the injectors. i ran a compression and all of them are at 110ish. im lost, i dont know what to do next? the computer? cam position sensor maybe? idk. the intake and injectors are off of the widnsor engine so i know they worked. the wiring is to so i dont know what is wrong. do i need to use the romeo wiring harness i have? will it even work? please any and all help would be appreciated, i'm just at the breaking point on this car and out of ideas.
 
There are 3 main connectors to the engine harness. A large square one, a smaller one and a round one. The cylinders that are misfiring have the same connector in common. Go back and double check that all of the connectors are fully inserted.

The connector likely missed is the large square one C133. Start by double checking the bolt has been fully tightened.

Double check the grounds. Especially the ground strap between the left hand motor mount and frame rail.
 
i never took off the large square one, i took everything from the driver side apart and laid it all over to the side. it came apart at the power distribution box. and how will i know if i have a bad ground? how can i check for that?
 
You removed an entire motor and never disconnected the motor wiring harness from the body? All I can say is WOW. This really opens up the possibility for wiring harness damage.

There is a bare grounding strap going from the left hand motor mount to the car's frame rail. The fact that you do not know what I'm talking about says that you did not know it is there. What typically happens is this ground strap is pulled free when the motor is removed. Since it was never disconnected, then the installer does not know to re-attach it.

Measure resistance from the alternator's case to the battery negative with the key off. Set the Ohm meter on it's lowest scale. Should be low. Post.

Let's back up a few steps. Confirm fuses F2.2 and F2.8 in the CJB. Not a bad idea to confirm all of the fuses in both fuse panels.

Next confirm +12 volts at each cylinder COP and injector red wires with the key on. If there are ANY without +12 volts, STOP and find out why.

Use a "noid" style test light to confirm an injector pulse on each cylinder. Repeat for each injector. Make note of which cylinders have a pulse. I think it's likely there is a combination of COP and fuel injectors not working. The noid test light will help determine what the combination really is.

If you need copies of Ford workshop manuals, wiring diagrams, and PCM manuals, I maybe able to help. PM if interested.
 
ok i know about the grounding strap on the frame rail, i removed it and put it back on when i pulled the motor and put it back on with the new one and its tight so its good. ill have to run out side and check the volts on cops and injectors. worse case its in the harness, can i use the 04 gt romeo harness? there is only one thing that i can see is different about it, and its a little sensor on the top of the passenger side vavle cover that is in the vent port right in the middle. and yea if you can send me some wiring digrams and what not, that would be awsome! thanks!
 
my multi meter is way out of calibration for some reason so i cant get a good reading on anything. as soon as i find one i can borrow i will take a reading on everything and let you know were everything is at. and let me know if i can use the new harness. thanks bro..