How about the water getting in the cylinder has done a little erosion on the bore , seen this a lot on the toyota lucidas when heads have been cracked, but would of thought you would have seen this on your strip down though
Water could have done some damage to injector nozzle, can you identfly which cylinder is missing with injector correction values ?

Try swapping an injector over to verify, maybe worth doing a compression test from cold.

We havent had any issues with cracked heads on thev td5 , someone else may know different