67 dart stroker hellcat gen3 hemi with twin turbos...

I have limited experience with Holley, but I have plenty of experience with Megasquirt. I once read if you think you have enough grounds with EFI, add more. Make sure the ground for the Holley goes to the battery. Also, make sure you have a good ground from the battery to the engine block, engine block to chassis, etc. I don't know how many grounds Holley has in their harness, but the sensor grounds should be common with the battery ground. Only way to do that is to tie everything together so you don't create a ground loop.
Also, is it possible for you to data log when the problem occurs? You should be able to look at cam and crank signal and see which one is going away.
The megasquirt software (Tunerstudio) has a function to look at both cam and crank signals at the same time while cranking. Does the Holley software have that function?