I wouldn't use the Holley throttle body. The injectors are known to go bad. They also seem to be difficult to tune with.

The PCM you have is meant to be use with an E trans. You will need to modify the BIN file right off the bat, snce you are using a non-E trans.

IIRC, you can use the 2 PPR VSS with this ECM, but the bin has to be set to "VSS not from DRAC". This setting should be in scalers (When using Tuner Pro). I used a 16197427 PCM in a conversion, and initially it was with a non-E trans, and used a 2 PPR VSS. This is a similar PCM to what you have.

What exactly did you have changed in the PCM to run 4 injectors? I've ran custom 4 bbl TBIs with bone stock PCMs without issue.