I went through a similar issue. I had a billet 24x wheel installed on my Eagle crankshaft. Also using Holley EFI. Anyway, the fucking thing would not start and was slipping in and out of sync while cranking. I was using the factory crank sensor, truck has less than 20k miles on it. Anyway, before tearing into complicated shit, I went to autozone and bought a replacement crank sensor. Threw it in and the thing fired right up. I then starting having issues with it loosing signal at 6500 rpm in boost and the ecu freaking out.
When LME installed the wheel on the crankshaft, it had a run out of .025". They told me that while they typically shoot for a better number than that, they assured me that it was well within an acceptable range and should work fine. Well, I later found out that .025" of run out is way on the high side. I chalked up the no start issue to be that the two crank sensor I had where just different enough for one to work and not the other. However, once I got into boost and 6500 rpm, the crank started flexing enough that nothing would fix it. Instead of pulling the motor down to find someone competent enough to install a new reluctor wheel, I just went to an external 4x flying magnet set up and all has been well since. The reason why I'm telling you this, it that I have seen first hand that a reluctor that is just on the verge of being out of spec that it can respond differently to different crank sensors.
When LME installed the wheel on the crankshaft, it had a run out of .025". They told me that while they typically shoot for a better number than that, they assured me that it was well within an acceptable range and should work fine. Well, I later found out that .025" of run out is way on the high side. I chalked up the no start issue to be that the two crank sensor I had where just different enough for one to work and not the other. However, once I got into boost and 6500 rpm, the crank started flexing enough that nothing would fix it. Instead of pulling the motor down to find someone competent enough to install a new reluctor wheel, I just went to an external 4x flying magnet set up and all has been well since. The reason why I'm telling you this, it that I have seen first hand that a reluctor that is just on the verge of being out of spec that it can respond differently to different crank sensors.