You really need to identify ALL of your modifications when reporting problems. The aftermarket flywheel has to be set up like the stock flywheel. You have to have the set screw for the reference signal the same height as the stock set screw. Measure off of the starter ring teeth. If not then you don't get any signal OR you take out the set screw (pin) and the sensor when they hit.
Here are the signals from the factory DME Testing Plans:
Reference: Set Screw-Pin
Speed: Starter Ring Teeth