Troubles after finally installing breathing equipment (5)
I believe the answer is:
gills
'breathing equipment' is the definition.
(fish breathe with gills)
'troubles after finally installing' is the wordplay.
'troubles' becomes 'ills' ('ill' can be a synonym of 'trouble').
'after' says to put letters next to each other.
'finally' suggests the final letters.
The last letter of 'installing' is 'g'.
'ills' put after 'g' is 'GILLS'.
(Other definitions for gills that I've seen before include "Quantities of drink" , "Fish breathe through them" .)