If you had the issue with the previous distributor and now with the EFI and a new ignition system (or at least the distributor) you need to look at what has remained the same. On the electrical side, are you using the same coil? I suspect that your issues more mechanical in nature, meaning the timing chain/gears. I understand you have a crate engine but that doesn't mean there isn't an issue.
Should you be concerned? Perhaps, depends on what is doing it. If it is a timing chain problem then yes you should. Drop the oil and see if there are any metal flakes in it. If there is, then you need to pull the front of the engine apart, if there isn't you may not be out of the woods, but you need to keep looking. another trick is to use a stethoscope (or long screw driver) on the timing chain cover and see if you can hear any weird noises.
All that said, I would look at everything connected to the timing side that has carried over.