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Eider, a small number of the normal clues have answers which are affected by the letter changes mentioned. Pencil/tippex is your friend! Personally, I just used ink but left room in each square for a possible alternative.

Crucifixion/lumen, what worked for me was cold solving a few across clues (especially 1, 12, 20) and some intersecting downs. That made it pretty obvious what the first “treatment” is, which helped in finding the letters for the first activity (a synonym of the treatment). That helps with identifying the surplus words - there are many red herrings! Once you know the first activity, the second is fairly obvious.

Cruciluci.. sorry about the auto-correct!

Thanks, Jack. You helped immensely,

I should have known to read the instructions several times when they were that long.
The two words were something I expected hours before the characters, but misread the preamble.

I'm still stuck on the parsing of two clues and stumped on two more, but it was very fun, and a favourite of my late father.

Glad it was of some use - and that you enjoyed the struggle.

Thanks Graham, you encouraged me to get stuck in (with ink!). All done now, a nice puzzle!

I've done what I believe to be required, but I'm left with a non-word at 26d (unless the name of a manufacturer of scened candles is permissible). Have I erred?

'Scented', not 'scened'. Apologies for the sloppiness.

Biggus56, my 26 D is a completely normal, valid word - an alternative spelling for a substance up in the atmosphere (and I think it has other meanings too, I can't check right now).

Finished grid fill now, and everything apart from phrase.
Know nothing about the subject...will now explore the two unclueds!
I have heard a slang phrase, 3,7, but cant find it anywhere, despite valiant help from drxx at Post 5. Is that the phrase I need?