I just had to do this -
don't use TDC as the reference when you drop it back in. I tried doing it using TDC as the mark and got engine codes and/or mediocre performance and hesitations.
This procedure is for a 3.0L built for the '04 model year.
You want to:
1. Remove spark plugs 2-6, and LOOSEN spark plug 1 a bit
2. Remove the crank position sensor - you'll see a boss with a line on it once it's removed which you will use to judge position off of. You may need to spray a little brake cleaner if it's gunked up.
3. Put it to TDC on the compression cycle(you'll hear a slight hiss and feel the pressure building up when you're hitting compression cycle), then slooowly move it 1 tooth further (each tooth is 10 degrees) to prep for reinsertion.
The gap in the teeth will NOT line up with the crank position sensor at TDC, you will see the 5th tooth pointing straight at the line when at TDC. The gap is there for visual lineup with something else.
4. I used a Cardone set that I borrowed from Autozone, if you use that one use the BLUE positioning tool. A correct tool(regardless of color) will hold the flag about 15-20 degrees off-center of the gap, do NOT use the tool that holds the flag on-center. That's for different, but related, engines. OTC Tools' number for the positioner is 6473, you can look at what its angle is on
Amazon.
5. Take the sensor cap off the CMP and set aside.
6. Affix the positioning tool to the CMP, point the arrow leftwards about 60-75 degrees, and start inserting. You'll probably have to wiggle a little bit to get it in, don't be surprised if you wind up a little left or a little right of the engine's centerline in the end. If you insert with the tool arrow pointed at the centerline, it'll end up way to the right.
7. Make sure the positioning tool doesn't come loose while inserting all the way, although the assembly will have a small bit of wiggle to it.
8. Tighten down the hold-down bolt to secure
9. Remove the alignment tool, and reinstall the sensor cap.
It helps greatly to remove the serpentine belt off of its top idler when you're attempting this, and to have a good bright light source as well.