I don't know who you are though. Are you a shop, a dealer?
There are a few main things that could be going on.
First would be the cam sensor's signal being open. Did you labscope at the PCM connector or the sensor? If you didn't check it at the PCM I would go there next.
Next would be damage to the crank sensor tone wheel or an incorrect tone wheel. If the crank tone wheel was damaged it could possibly do this, and if the incorrect crank with a different tone wheel was installed for some reason then it will do this. 2003 engines were controlled by an SBEC engine controller, the 2003.5 engines are NGC controlled.
The same goes for the cam sensor magnet. It's going to be different for SBEC and NGC.
If you had an aftermarket timing belt
or timing components that aren't quite built to specs, or components are mismatched so the engine isn't in time it will do this.
One common mistake while assembling these is using an impact to tighten the cam sprocket bolts. This will shear the dowel pins, throwing off the cam's alignment to the sprocket. If the sprockets weren't held stationary and a torque wrench used for tightening then this is highly suspect.
Another possibility would be machining the head. Machining the head makes it thinner, dropping the cam's centerline closer to the crankshaft. This throws off the cam timing. On an overhead cam engine machining the head can get you into trouble with setting cam sensor or cam/crank misalignment codes, and can cause some driveability issues even without codes.
The first thing that needed to be done upon reassembling the engine would be to do a cam/crank relearn with a DRBIII scan tool. This allows the engine controller to relearn and compensate for many of these things I've mentioned. The first thing I would recommend doing now would be to have the cam/crank relearn done and see if the problem goes away.