Very very hard for timing chain to jump a tooth, never even heard of that happening on a 2.9l
If valve timing is off("jumped tooth"), then that will lower compression, engine would still run OK, no missing, but would be sluggish for power.
You can check vacuum level at idle, 17"-21" would be OK, less could mean low compression, so compression test would be next.
Check the vacuum hose on the Fuel Pressure Regulator(FPR), if FPR is leaking that vacuum hose will have fuel inside it and it would be sucked into engine causing engine to run rich and stumble.