Yes 45 dist degrees is 90 at crank.

OK so "the timing you see" meaning you are checking timing with a timing light? Is that with a dial back light or a fully degreed balancer? Did you verify that TDC mark is correct?

Third paragraph is expected.
That last statement about the variable distance between sensor and rotor is a bit confusing. Do you mean that one flag or gap on the shutter is a different size than the others? That's how most other systems determine #1 location.
This implies you are going SFI vs batch fire, is that correct?