Hi, s_pugh,
I didn't finish this puzzle until about 1AM this morning, and I'm still not sure how to parse the wordplay in 2d and 20d.
As has already been noted in this forum, there are two cells on the NW-SE diagonal where there is a letter clash before the letters are replaced. One of these is the fifth cell of 24d, which is the ninth cell of 34a. The two letters clashing in this cell are both followed by the same letter in the theme word, so that resolves the clash. Of the two possibilities for the fifth letter of 24d, both are in the theme word, but only one is followed by the same letter as the letter that follows the letter in the ninth cell of 34a (sorry, that sounds very complicated).