Hi ninacross, the clean-up instruction is only the first four words arising from the dropped letters. The trail of knight’s moves begins with the first letter of the work area, goes through seven cells where the across and down entries clash, and ends with the last letter of the perpetrator. The nine letters consisting of the first letter of the work area, the seven letters from the across entries in the clashing cells, and the last letter of the perpetrator, spell out “dark brown”, which has already been noted in an earlier post as the “tone” for the work area.
The cell where 42d and 49a intersect is a clash of “I” from the across clue and “DOT” from the down clue, and these can be combined to form a pling (word remembered from Listener 4418 last year = “!”). “Missing the point” in that cell gives 49a as “TEPID” and 38d as “BARI”, the latter being a real name (of a city in Italy).
The instruction given by the last three words from the dropped letters tells you what seven letters (not nine, as the first and last letters in the trail don't clash), in an order that has to be worked out, will replace the same number of letters in column 3. This leads to a four-letter warning, beginning with the fourth letter of 3d, running down to the third letter of 48a, turning through 90 degrees and running along the bottom row, including the eight letters of the work area and the cell with the exclamation mark (a total of 19 cells). Not all of the letters in column 3 that form part of the message need to be replaced, only a subset of consecutive letters. However, one of this subset of consecutive letters that have to be replaced is actually “replaced” with the same letter. Remember that all the words in the final grid are real words or real names, and this will give you hints for which set of consecutive letters in column 3 can be changed, and which have to stay the same.
I thought that this puzzle had a good set of clues, but the endgame was over-elaborate (hence this long post) and the end product a bit of an anti-climax.