Uncomfortable pain: one might be running? (6)
I believe the answer is:
stitch
I believe this clue is a double definition.
'uncomfortable pain' is the first definition.
(stitch is a type of pain)
'one might be running?' is the second definition.
(running stitch is a type of stitch in sewing)
(Other definitions for stitch that I've seen before include "One in time is said to save nine" , "Sewing loop and sharp pain in the side" , "Link, loop or knot made in knitting or sewing" , "something seen in the needlework class" , "Surgical suture" .)