Organ with a switch finally stuck in church -- it's a pain (7)
I believe the answer is:
earache
'a pain' is the definition.
(earache is a kind of pain)
'organ with a switch finally stuck in church' is the wordplay.
'organ with' becomes 'ear' (I am not sure about this - if you are sure you should give a lot more credence to this answer).
'finally' says to take the final letters.
'stuck in' indicates putting letters inside.
'church' becomes 'ce' (abbreviation for Church of England).
The last letter of 'switch' is 'h'.
'h' put inside 'ce' is 'che'.
'ear'+'a'+'che'='EARACHE'
'it's' acts as a link.
Can you help me to learn more?
(Other definitions for earache that I've seen before include "Aural discomfort" , "Otalgia" , "Form of torture" , "complaint to The Listener" , "listener's discomfort" .)