2001 Oldsmobile Alero DTC

I rebuilt my 2001 Alero after a leaking lower intake problem. Had all parts cleaned at the machine shop, replaced all pistons, etc. Replaced entire fuel rail (injectors, regulater.) With new. Started with a miss ans DTC for random misfire, no. 3 and no. 5 misfire. Checked everything out, injectors 3 & 5 were crossed - corrected that. Still get random or no. 3 misfire.
Had fuel system fully cleaned by GM, serviced and checked. They reported great power, vacuum, compression and starting, but still a small miss that didn't trip the computer - no explaination. Drove home, same DTC, random or no. 3 misfire. All plugs, wires and coils are new. Coils show resistance within spec, wires too high. Replaced again with Autolite pro and Platinum. All sensors are new, replaced IAC again anyway - same DTC.

Considering possible damage to the ring gear on the harmonic balancer sending a srewy crankshaft position signal, or possibly defective module/controller under the coils.

Any help/suggestions?

Thanks,

Robbie Neal