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Thanks Will37. I had not come across that term for vessel before although it rings a vague bell from Biology lessons.

Re 41d, R = recipe, take (Latin) + word for chances, gambles (middle letter is extra) all reversed

Thank you Dodgepot. What a fiendishly deceptive clue. I don't think I would ever have seen past 'take chances' giving the 4 letter verb.

It is clever. They are known as “lift and separate” clues, where a phrase in common parlance has to be split up in order to make sense of the clue. This is the history, with a few examples:

https://www.crosswordunclued.com/2010/12/lift-and-separate.html?m=1

Thank you, Dodgepot, for 41d. That thumping noise you can hear is me kicking myself for having failed to parse it.

can anyone tell my why i've got three unused extra letters from the down clues?

All of the extra letters from down clues are used in the instruction (there is no extra letter in the anagram clue, of course). If you say which clues you think have redundant extra letters, we may be able to clarify.

30 down clues, 29 extra letters, 26 replacements in the grid

The first three letters are an instruction and don't appear in the grid.

All finished now. Amazing construction!

Only slight worry is 28d - does it have some significance that has flown high above my head?