The earlier models were alignment versions. The Series II motors 95-05 NA and 96-03 SC do not require any alignment.
I've had the intermittant CKP issue in my car'* long past and it'* a pain. Nothing really says "change this sensor" and the car still seems to run pretty well. I took the chance on the $25 for the sensor and life has been great since. I'd suggest the sensor chance, but good diagnositics would put cleaning and general lookover first.
Very tough to see in this picture is the fine metal particles that are stuck in between the fingers that read the holes on the back of the harmonic balancer. I believed this to be the issue.
Due to the shield you can't get a good stream of water or air into the area to clean the sensor w/o removing the HB.