Substance found in morning is troublesome (4)
I believe the answer is:
gist
'substance' is the definition.
(I know that substance can be written as gist)
'in morning is troublesome' is the wordplay.
'in' indicates the answer is hidden within the clue.
'GIST' is hidden within 'morning is troublesome'.
'found' is the link.
(Other definitions for gist that I've seen before include "Main idea, kernel of matter" , "General meaning or main point" , "Basic meaning" , "Significance" , "Drift" .)