From what you describe, it is pretty likely that cam timing is one tooth off, and/or your IP timing is *way* off (maybe 15-18 degrees, about 1 'tooth', and requires pump R&R to correct.) I've done this job and I know how easy it is for the cam, crank, and IP timing to get out of sync. If you didn't check this by rotating the engine multiple times when the head was installed, verifying cam timing first, and IP timing second... well... you'll see.

Electrical problems, or internal IP issues, are MUCH less likely (IMO). That is unless you fiddled with IP delivery valve seals or something, but it doesn't sound like it - I got the impression the IP went to a diesel shop and came back 'fixed', and you just popped it in place. (And that's exactly when the timing got off...)