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And now all done. Thank you, Ifor. Great construction.

OK, I have a full grid and still mystified. Can someone please translate preamble, especially reference to 1st manipulation?

It's that old chestnut "elements" again

I came late to this and despite all the as usual very useful hints in this thread I am still none the wiser about the endgame. I think that the definition of the missing letter required refers to chemical elements and also that it is the word defined in the clue rather than the one given by the wordplay which is entered in the grid. After that I am totally confused by the reference to the first manipulation let alone any further manipulation which follows that. I am just about to go back through it to make sure I have the right letters in the bottom row. Currently I have 9 different ones.

In each square with 2 letters look up the letters in the periodic
table to get the atomic numbers of the elements concerned.
Subtract the smaller from the larger. Sometimes you might get a number higher than 26, if so reduce the number by 26 or a multiple of
26. Convert the number from 1 to 26 into the letter a to z.
Put it in the grid at the bottom. A suitable word will appear.

Thank you for that Krauton. It will give me something t work on later. Fingers crossed I have the right clashing letters in each case.

I have gone badly wrong with this. Following Krauton's excellent advice I have finished up with RNTITNUAUTMAO which is not remotely like a word. Also I am still far from clear if it is the defined word or the one produced by the wordplay which is entered in the grid.

ap, if you read the preamble carefully you should see which of the clashing letters goes in the grid.

some of the letters are correct but mostly not..
1st clash is in 11d Y and K .....Y..39 in the table ....K 19 in table ...difference 20 which gives T for the first letter in the bottom row

Thank you Son1ofRover1 and Kirky. I really am losing the plot. I was looking at the letters on clue order rather than column order and a bad piece of mental arithmetic didn't help. I will get back to it later.