Close to tears, short person in pain from running (6)
I believe the answer is:
stitch
'pain from running' is the definition.
(pain caused when running)
'close to tears short person' is the wordplay.
'close to' suggests the final letters (the close/ending of).
'short person' becomes 'titch' (titch can informally mean a small person).
The final letter of 'tears' is 's'.
's'+'titch'='STITCH'
'in' is the link.
(Other definitions for stitch that I've seen before include "Pain for runner" , "Sew - sharp pain in side" , "A result of running" , "Sharp pain in side of body caused by exercise" , "A sewer may produce such" .)