1994 Saturn SL1 will a 2000 engine Fit a 1994

I put a 2000 sl1 engine head and block in my 94. I transferred intake and manifold. Now I have a ignition code popping up. I was told it was because the cranks are different. I used the 1994 blown up engines cam sensor, will useing the 2000 cam sensor fix my problem or is there a way of fixing it. The car runs fine.