Hello Crackability.
Remaining two clashes are:
3rd in 48a
2nd in 47a
The losing letters are the ones which complete the words in the messages. There are two letters missing from the last word of the across message and one each from the first, second and fifth words of the down message. I have left the other clashing letters where they are in the grid leading to various non-words. I can't work out what you have to do in the rectangle - whatever it is it might resolve the non-word thing.