I finally got time to reinstall the engine and it fired right up. The timing diagram I attached is for a V3307-CR-TE4B and V3307-CR-TIE4B only and was slightly hard to find. Other 'generations' have dissimilar alignment marks. If you look at the good & bad waveforms long enough, I think it is conclusive that injection events were firing on exhaust strokes, the cam was correctly synced to the crank which is why there was good compression, but with the crank position being inferred from the reluctor on the HPFP, the ECM was being fooled. The engine runs surprisingly well, I ran it through some paces to break it in and all is well that ends well.