Hard start/misfire help

Just finished rebuilding 2004 Dodge Stratus DOHC 2.4L engine (timing belt broke). Just about every engine part was either replaced, rebuilt, or reworked. It starts (very difficult) but cylinders 2,3 & 4 are misfiring. #1 plug is clean but the rest have a heavy carbon residue & are gas soaked. Double & triple checked the timing, both marks on the cam pulley are aligned at TDC. There appears to be enough spark. Scanner only gives a code P0016 (Cam/Crank Position Correlation Sensor A - Bank 1) & it's only reading temp sensors, not any other vital sensors. Normally if the Cam or Crank sensor is not working the car won't start at all? So either there is one other sensor bad or when the shop pulled the crank gear (that the sensor reads) off to put it on the new crank, it was put on in the wrong position (is that possible). However, if it is anything like the flywheel, it can only go on one way. Any ideas? Help? Thank-you.

I would use a wiring diagram and make sure the injector wires are on the correct injector. I would also make the plug wires are on the correct spark plug.
You could have a bad pressure regulator for the fuel system make sure the vacuum is connected to it. Make sure all plugs are installed on the wiring harness.
Start with the basics first.