I agree on the burning bits being loose stuff in the exhaust from being shaken around taking it apart and putting back together. I've seen it.
No power? Not sure from here is everything back in its original place? Did you have the cam out? I would need to look that engine up to see what sets timing and injector adjustment. Some are very touchy if the injector timing and adjustment is set by the cam.
Been a lot of year since I did the diesel tractor engines. Outside jumping a 4020 last weekend.