It's likely that you've not damaged anything so don't worry too much. Just make sure you use a fresh washer, as the whole point of them is that they crush and deform to fill any grooves etc in the mating faces. Once they've crushed down once they won't seal effectively again.
When I did mine, there was loads of crud at the bottom of the bore, so I attached a little pipe (think air line) to the Dyson and pushed that into the bore, then scraped GENTLY with a flat blade screwdriver to get rid of the carbon etc. Make sure you get rid of any carbon build up on the sealing face of the injector too.
After that I took a 10 or 12mm wood dowel and taped some fine grade wet'n'dry to the end, then gave it a gentle lapping for a few seconds like you would do if you were lapping a valve.
I seem to remember that when I did my injectors (installed new nozzles) they initially were a little more noisy than they were before, but I had them checked by a local diesel specialist and he said they were working perfectly (and still are now), it will always sound worse if it's only 1 making the racket. To be honest, with my engine on 289,000 miles, the noisy injectors are probably the quietest things in the engine.
Good luck mate, keep us informed
Dave.