Since it seems like everyone else missed the 'TOS' part of your request, here's some TOS fics with hurt Kirk. (I don't really pay that much attention to who does what in sex scenes, so I can't promise bottom Kirk, but I hope this is is helpful to you anyway.) They're all K/S except the last one which is gen.

Little Sorrows by Dovya Blacque (http://www.ksarchive.com/viewstory.php?sid=2601) (I particularly like this one, Kirk suffers from a broken mindlink with an old friend)
Predawn by Mary Kay (http://www.ksarchive.com/viewstory.php?sid=3894) (Kirk goes back in time)
Something by Mary Kay (http://www.ksarchive.com/viewstory.php?sid=3792) (Kirk is attacked by his own guilt)
Missing In Action by Rae Trail (http://www.ksarchive.com/viewstory.php?sid=4840) (amnesia)
In the After Silence by isabol (http://www.ksarchive.com/viewstory.php?sid=2009) (post "Turnabout Intruder")
A Light in the Darkness by Debbie C (http://www.ksarchive.com/viewstory.php?sid=799) (Kirk is injured on shore leave)
Strong Together by UKJess (http://www.ksarchive.com/viewstory.php?sid=463) (prostitution and references to Tarsus, you might have already read it)
Nightvisions by Carol A Frisbie and Susan K James (http://www.ksarchive.com/viewstory.php?sid=4332) (blindness, very long)
Thy Brother by MissAnnThropic (https://www.fanfiction.net/s/2191170/1/Thy-Brother) (Kirk is injured protecting Spock)