Join up, pain though it is (6)
I believe the answer is:
stitch
'join' is the definition.
(thesaurus)
I cannot understand how the rest of the clue works.
Can you help me to learn more?
(Other definitions for stitch that I've seen before include "Pain in the side brought on by exercise" , "Tack; pain in side" , "herringbone?" , "One's in time to save eight others" , "something seen in the needlework class" .)