Ref Sync Errors

[92SS3908]

Brief background on the setup: Honda F4i running the M400. The ref and sync sensors are the stock magnetic sensors. The ref trigger wheel is stock and the sync wheel on the cam started as the stock wheel but I cut off two of the three teeth to give one pulse per cycle.

I am getting errors that include the following:
Error No Ref Signal
Error Ref Noise Ar
Error Ref Noise Tr
Error Ref Runt
Error Ref Low Level
Error Sync Runt

Ref Sync capture looks clean I have attached a screenshot.

Based on the data log many of these errors occur during cranking or when shutting down the engine however I am consistently getting Error Sync Runt while the engine is running and many times getting Error Ref Runt while the engine is running. I have also attached a data log.

The engine runs but very poorly. Seems like it is missing and you have to keep it going with the throttle or it will die. Throttle response is almost nonexistent. EGTs are cold: between 800 and 1100, by backing the timing down EGTs can get up to 1200 but the engine still struggles to run. I have put a timing light on it while cranking and with the test advance set to zero all cylinders appear to be firing at the correct time. It is also advancing in the correct direction.

Any help would be greatly appreciated.
Thanks in advance

[OmarK]

I think you should take a look at the ECU seminar notes which will give you a description for each of those errors and also gives you advice on setting changes you can make...