You just about have the ref/sync thing sorted except the REFerence tooth (the one the CRIP is calculated from) does not have to be 90 before TDC. They want the missing teeth located there on a missing tooth wheel because this is where the speed is greatest and the acceleration is lowest giving the most reliable sensing of the missing teeth. On a multitooth mode (12 even on the crank) you can choose whichever one you want as the reference tooth by placing the sync in front of it.
For your starting issue assuming a 12 tooth wheel - try phasing the trigger wheel on the crank so that a tooth is aligned with the sensor at about 10-15 BTDC. At low RPM the ECU will trigger on the tooth edge not necessarily the table value. So having a tooth in about the right spot for cranking timing will be helpful.
So assuming you have a tooth at 45 before, 15 before, 15 after etc I would set the sync signal so that it is aligned at either 60 BTDC, 30 BTDC, TDC, or 30 ATDC etc.
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