I’m tearing my hair out with this puzzle now.
I’ve applied the replacement as per my interpretation of the message from the extra letters. It was looking good as these replacements were all cross-checking nicely… and then I hit some clashes (6 cells). I have checked them numerous times. My ‘letters that have no such replacement’ are gobbledegook. But I must’ve done something right as the row by row message makes sense and, I think, I’ve applied that correctly.
I appreciate it might be difficult to reply to this without revealing too much so, if that’s the case, don’t worry. Thank you all for letting me vent before potentially throwing in the towel.